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Tseng WC, Munisha M, Gutierrez JB, Dougan ST. Establishment of the Vertebrate Germ Layers. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 953:307-381. [PMID: 27975275 DOI: 10.1007/978-3-319-46095-6_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The process of germ layer formation is a universal feature of animal development. The germ layers separate the cells that produce the internal organs and tissues from those that produce the nervous system and outer tissues. Their discovery in the early nineteenth century transformed embryology from a purely descriptive field into a rigorous scientific discipline, in which hypotheses could be tested by observation and experimentation. By systematically addressing the questions of how the germ layers are formed and how they generate overall body plan, scientists have made fundamental contributions to the fields of evolution, cell signaling, morphogenesis, and stem cell biology. At each step, this work was advanced by the development of innovative methods of observing cell behavior in vivo and in culture. Here, we take an historical approach to describe our current understanding of vertebrate germ layer formation as it relates to the long-standing questions of developmental biology. By comparing how germ layers form in distantly related vertebrate species, we find that highly conserved molecular pathways can be adapted to perform the same function in dramatically different embryonic environments.
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Affiliation(s)
- Wei-Chia Tseng
- Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Mumingjiang Munisha
- Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Juan B Gutierrez
- Department of Mathematics, University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Scott T Dougan
- Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA.
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Gupta HR, Patil Y, Singh D, Thakur M. Embryonic Zebrafish Model - A Well-Established Method for Rapidly Assessing the Toxicity of Homeopathic Drugs: - Toxicity Evaluation of Homeopathic Drugs Using Zebrafish Embryo Model. J Pharmacopuncture 2016; 19:319-328. [PMID: 28127503 PMCID: PMC5241443 DOI: 10.3831/kpi.2016.19.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 12/01/2016] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES Advancements in nanotechnology have led to nanoparticle (NP) use in various fields of medicine. Although the potential of NPs is promising, the lack of documented evidence on the toxicological effects of NPs is concerning. A few studies have documented that homeopathy uses NPs. Unfortunately, very few sound scientific studies have explored the toxic effects of homeopathic drugs. Citing this lack of high-quality scientific evidence, regulatory agencies have been reluctant to endorse homeopathic treatment as an alternative or adjunct treatment. This study aimed to enhance our insight into the impact of commercially-available homeopathic drugs, to study the presence of NPs in those drugs and any deleterious effects they might have, and to determine the distribution pattern of NPs in zebrafish embryos (Danio rerio). METHODS Homeopathic dilutions were studied using high-resolution transmission electron microscopy with selected area electron diffraction (SAED). For the toxicity assessment on Zebrafish, embryos were exposed to a test solution from 4 - 6 hours post-fertilization, and embryos/larvae were assessed up to 5 days post-fertilization (dpf) for viability and morphology. Toxicity was recorded in terms of mortality, hatching delay, phenotypic defects and metal accumulation. Around 5 dpf was found to be the optimum developmental stage for evaluation. RESULTS The present study aimed to conclusively prove the presence of NPs in all high dilutions of homeopathic drugs. Embryonic zebrafish were exposed to three homeopathic drugs with two potencies (30CH, 200CH) during early embryogenesis. The resulting morphological and cellular responses were observed. Exposure to these potencies produced no visibly significant malformations, pericardial edema, and mortality and no necrotic and apoptotic cellular death. CONCLUSION Our findings clearly demonstrate that no toxic effects were observed for these three homeopathic drugs at the potencies and exposure times used in this study. The embryonic zebrafish model is recommended as a well-established method for rapidly assessing the toxicity of homeopathic drugs.
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Affiliation(s)
- Himanshu R Gupta
- Department of Medical Genetics, MGMIUDBS, Mahatma Gandhi Mission Institute of Health Sciences, Kamothe, Navi Mumbai, India
| | - Yogesh Patil
- MGMCET & Central Research Laboratory, Mahatma Gandhi Mission Institute for Health Sciences, Kamothe, Navi Mumbai, India
| | - Dipty Singh
- National Centre for Preclinical Reproductive and Genetic Toxicology (NIRRH), National Institute of Research in Reproductive Health (ICMR), Jehangir Merwanji Street, Parel, Mumbai, India
| | - Mansee Thakur
- Mahatma Gandhi Mission College of Engineering and Technology & Department of Medical Biotechnology, Central Research Laboratory, MGM Medical College, MGMIHS, Kamothe, Navi Mumbai, India
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103
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Schartl M, Walter RB. Xiphophorus and Medaka Cancer Models. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 916:531-52. [PMID: 27165369 DOI: 10.1007/978-3-319-30654-4_23] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Besides recently developed zebrafish cancer models, other fish species have been employed for many years as cancer models in laboratory studies. Two models, namely in Xiphophorus and medaka have proven useful in providing important clues to cancer etiology. Medaka is a complementary model to zebrafish in many areas of research since it offers similar resources and experimental tools. Xiphophorus provides the advantages of a natural ("evolutionary mutant") model with established genetics. Xiphophorus hybrids can develop spontaneous and radiation or carcinogen induced cancers. This chapter describes the tumor models in both species, which mainly focus on melanoma, and summarizes the main findings and future research directions.
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Affiliation(s)
- Manfred Schartl
- Physiologische Chemie, Universität Würzburg, Biozentrum, Am Hubland, D-97074, Würzburg, Germany. .,Texas Institute for Advanced Study and Department of Biology, Texas A&M University, 100 Butler Hall, College Station, Texas, 77843-3258, USA.
| | - Ronald B Walter
- Chemistry and Biochemistry, 419A Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX, 78666-4616, USA
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104
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Elks PM, Renshaw SA, Meijer AH, Walmsley SR, van Eeden FJ. Exploring the HIFs, buts and maybes of hypoxia signalling in disease: lessons from zebrafish models. Dis Model Mech 2016; 8:1349-60. [PMID: 26512123 PMCID: PMC4631790 DOI: 10.1242/dmm.021865] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A low level of tissue oxygen (hypoxia) is a physiological feature of a wide range of diseases, from cancer to infection. Cellular hypoxia is sensed by oxygen-sensitive hydroxylase enzymes, which regulate the protein stability of hypoxia-inducible factor α (HIF-α) transcription factors. When stabilised, HIF-α binds with its cofactors to HIF-responsive elements (HREs) in the promoters of target genes to coordinate a wide-ranging transcriptional programme in response to the hypoxic environment. This year marks the 20th anniversary of the discovery of the HIF-1α transcription factor, and in recent years the HIF-mediated hypoxia response is being increasingly recognised as an important process in determining the outcome of diseases such as cancer, inflammatory disease and bacterial infections. Animal models have shed light on the roles of HIF in disease and have uncovered intricate control mechanisms that involve multiple cell types, observations that might have been missed in simpler in vitro systems. These findings highlight the need for new whole-organism models of disease to elucidate these complex regulatory mechanisms. In this Review, we discuss recent advances in our understanding of hypoxia and HIFs in disease that have emerged from studies of zebrafish disease models. Findings from such models identify HIF as an integral player in the disease processes. They also highlight HIF pathway components and their targets as potential therapeutic targets against conditions that range from cancers to infectious disease. Summary: Hypoxia signalling, mediated by HIF, is a crucial pathway in many disease processes. Here, we review current knowledge of HIF signalling and disease, focusing on recent findings from zebrafish models.
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Affiliation(s)
- Philip M Elks
- Department of Infection and Immunity, Medical School, The University of Sheffield, Sheffield, S10 2RX, UK The Bateson Centre, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Stephen A Renshaw
- Department of Infection and Immunity, Medical School, The University of Sheffield, Sheffield, S10 2RX, UK The Bateson Centre, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Annemarie H Meijer
- Institute of Biology, Leiden University, 2333 CC Leiden, The Netherlands
| | - Sarah R Walmsley
- MRC Centre for Inflammation Research, University of Edinburgh, Edinburgh, EH16 4TJ, UK
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Abdelrasoul GN, Magrassi R, Dante S, d'Amora M, d'Abbusco MS, Pellegrino T, Diaspro A. PEGylated gold nanorods as optical trackers for biomedical applications: an in vivo and in vitro comparative study. NANOTECHNOLOGY 2016; 27:255101. [PMID: 27176116 DOI: 10.1088/0957-4484/27/25/255101] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Gold nanorods (AuNRs) are eligible for a variety of biological applications including cell imaging, sensing, and photothermal therapy thanks to their optical properties. The aim of this work is to show how AuNRs could be employed as non-photobleachable optical contrast agents for biomedical applications. In order to demonstrate the feasibility of their use as optical trackers, we employed two-photon emission confocal microscopy on cells incubated with PEGylated AuNRs. Remarkably, AuNRs were localized mostly in the perinuclear zone and microscopy characterization showed the presence of a considerable number of rods inside cell nuclei. Furthermore, we estimated the toxicity and the efficiency of cellular uptake of the PEGylated AuNRs as a function of administered dose on HeLa/3T3 cell lines and on zebrafish during development, employed as an in vivo model. Eventually, we observed good agreement between in vivo and in vitro experiments. The employed AuNRs were prepared through a photochemical protocol here improved by tuning the amount of the cationic surfactant cetyltrimethylammonium bromide for the achievement of AuNRs at two different aspect ratios. Furthermore we also investigated if the AuNR aspect ratio influenced the toxicity and the efficiency of cellular uptake of the PEGylated AuNRs in HeLa/3T3 cell lines and in zebrafish embryos.
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Patten SA, Parker JA, Wen XY, Drapeau P. Simple animal models for amyotrophic lateral sclerosis drug discovery. Expert Opin Drug Discov 2016; 11:797-804. [DOI: 10.1080/17460441.2016.1196183] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Brunet FG, Volff JN, Schartl M. Whole Genome Duplications Shaped the Receptor Tyrosine Kinase Repertoire of Jawed Vertebrates. Genome Biol Evol 2016; 8:1600-13. [PMID: 27260203 PMCID: PMC4898815 DOI: 10.1093/gbe/evw103] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The receptor tyrosine kinase (RTK) gene family, involved primarily in cell growth and differentiation, comprises proteins with a common enzymatic tyrosine kinase intracellular domain adjacent to a transmembrane region. The amino-terminal portion of RTKs is extracellular and made of different domains, the combination of which characterizes each of the 20 RTK subfamilies among mammals. We analyzed a total of 7,376 RTK sequences among 143 vertebrate species to provide here the first comprehensive census of the jawed vertebrate repertoire. We ascertained the 58 genes previously described in the human and mouse genomes and established their phylogenetic relationships. We also identified five additional RTKs amounting to a total of 63 genes in jawed vertebrates. We found that the vertebrate RTK gene family has been shaped by the two successive rounds of whole genome duplications (WGD) called 1R and 2R (1R/2R) that occurred at the base of the vertebrates. In addition, the Vegfr and Ephrin receptor subfamilies were expanded by single gene duplications. In teleost fish, 23 additional RTK genes have been retained after another expansion through the fish-specific third round (3R) of WGD. Several lineage-specific gene losses were observed. For instance, birds have lost three RTKs, and different genes are missing in several fish sublineages. The RTK gene family presents an unusual high gene retention rate from the vertebrate WGDs (58.75% after 1R/2R, 64.4% after 3R), resulting in an expansion that might be correlated with the evolution of complexity of vertebrate cellular communication and intracellular signaling.
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Affiliation(s)
- Frédéric G Brunet
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, UMR5242 CNRS, Université Claude Bernard Lyon I, Lyon, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, UMR5242 CNRS, Université Claude Bernard Lyon I, Lyon, France
| | - Manfred Schartl
- Physiologische Chemie, Biozentrum, University of Würzburg, Am Hubland, and Comprehensive Cancer Center, University Clinic Würzburg, Würzburg, Germany Texas Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, USA
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108
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Azizi S, Nematollahi MA, Mojazi Amiri B, Vélez EJ, Salmerón C, Chan SJ, Navarro I, Capilla E, Gutiérrez J. IGF-I and IGF-II effects on local IGF system and signaling pathways in gilthead sea bream (Sparus aurata) cultured myocytes. Gen Comp Endocrinol 2016; 232:7-16. [PMID: 26602376 DOI: 10.1016/j.ygcen.2015.11.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 11/13/2015] [Accepted: 11/17/2015] [Indexed: 12/22/2022]
Abstract
The insulin-like growth factors (IGFs) have a fundamental role in a vast range of functions acting through a tyrosine-kinase receptor (IGF-IR). IGFs in muscle can affect the expression of components of the local IGF system, myogenic regulatory factors (MRFs), proliferating (proliferating cell nuclear antigen, PCNA) or differentiating molecules (myosin heavy chain, MHC) and, lead to the activation of different signaling pathways. The response of all these genes to IGFs incubation at two different times in day 4 cultured myocytes of gilthead sea bream was analyzed. Both IGFs increased the expression of IGF-I and IGFBP-5, but showed different effects on the receptors, with IGF-I suppressing the expression of both isoforms (IGF-IRa and IGF-IRb) and IGF-II up-regulating only IGF-IRb. Moreover, the protein levels of PCNA and target of rapamycin (TOR) increased after IGF-II incubation, although a decline in Myf5 and a rise in MHC gene expression was caused by IGF-I. Taken together, these results provide evidence for the importance of IGFs on controlling muscle development and growth in gilthead sea bream and suggest that each IGF may be preferentially acting through a specific IGF-IR. Moreover, the data support the hypothesis that IGF-II has a more important role during proliferation, whereas IGF-I seems to be relevant for the differentiation phase of myogenesis.
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Affiliation(s)
- Sheida Azizi
- Department of Fisheries Sciences, Faculty of Natural Resources, University of Tehran, Karaj, Iran; Departament de Fisiologia i Immunologia, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Mohammad Ali Nematollahi
- Department of Fisheries Sciences, Faculty of Natural Resources, University of Tehran, Karaj, Iran.
| | - Bagher Mojazi Amiri
- Department of Fisheries Sciences, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | - Emilio J Vélez
- Departament de Fisiologia i Immunologia, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Cristina Salmerón
- Departament de Fisiologia i Immunologia, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Shu Jin Chan
- Departments of Biochemistry, and Molecular Biology and Medicine, The Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA
| | - Isabel Navarro
- Departament de Fisiologia i Immunologia, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Encarnación Capilla
- Departament de Fisiologia i Immunologia, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Joaquim Gutiérrez
- Departament de Fisiologia i Immunologia, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain.
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A new problem with cross-species amplification of microsatellites: generation of non-homologous products. DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2016; 31:131-40. [PMID: 20545002 DOI: 10.3724/sp.j.1141.2010.02131] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Microsatellites have been widely used in studies on population genetics, ecology and evolutionary biology. However, microsatellites are not always available for the species to be studied and their isolation could be time-consuming. In order to save time and effort researchers often rely on cross-species amplification. We revealed a new problem of microsatellite cross-species amplification in addition to size homoplasy by analyzing the sequences of electromorphs from seven catfish species belonging to three different families (Clariidae, Heteropneustidae and Pimelodidae). A total of 50 different electromorphs were amplified from the seven catfish species by using primers for 4 microsatellite loci isolated from the species Clarias batrachus. Two hundred and forty PCR-products representing all 50 electromorphs were sequenced and analyzed. Primers for two loci amplified specific products from orthologous loci in all species tested, whereas primers for the other two loci produced specific and polymorphic bands from some non-orthologous loci, even in closely related non-source species. Size homoplasy within the source species was not obvious, whereas extensive size homoplasy across species were detected at three loci, but not at the fourth one. These data suggest that amplification of products from non-orthologous loci and appearance of size homoplasy by cross-amplification are locus dependent, and do not reflect phylogenetic relationship. Amplification of non-orthologous loci and appearance of size homoplasy will lead to obvious complications in phylogenetic interference, population genetic and evolutionary studies. Therefore, we propose that sequence analysis of cross-amplification products should be conducted prior to application of cross-species amplification of microsatellites.
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110
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Mirsaeidi M, Gidfar S, Vu A, Schraufnagel D. Annexins family: insights into their functions and potential role in pathogenesis of sarcoidosis. J Transl Med 2016; 14:89. [PMID: 27071553 PMCID: PMC4830063 DOI: 10.1186/s12967-016-0843-7] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 03/30/2016] [Indexed: 12/13/2022] Open
Abstract
Annexins are Ca2+-regulated phospholipid-binding proteins that play an important role in the cell life cycle, exocytosis, and apoptosis. Annexin A11 is one of the oldest vertebrate annexins that has a crucial role in sarcoidosis pathogenesis. The mechanism of effect in sarcoidosis granuloma cells may be due to alterations in apoptosis. Immune cells with a specific mutation at protein location 230 are resistant to apoptosis and consequently have continued effects on inflammation and progression of sarcoidosis. The mechanism of action of annexin A11 may be based upon alterations in delivering calcium to two different apoptosis pathways (caspase and P53).
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Affiliation(s)
- Mehdi Mirsaeidi
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Miami, Miller School of Medicine, 1600 NW 10th Ave # 7060A, Miami, FL, 33136, USA.
| | - Sanaz Gidfar
- Department of Ophthalmology, University of Illinois at Chicago, Chicago, IL, USA
| | - Ann Vu
- Department of Medicine, University of Miami, Miami, FL, USA
| | - Dean Schraufnagel
- Division of Pulmonary and Critical Care, University of Illinois at Chicago, Chicago, IL, USA
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111
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Oliver VF, van Bysterveldt KA, Cadzow M, Steger B, Romano V, Markie D, Hewitt AW, Mackey DA, Willoughby CE, Sherwin T, Crosier PS, McGhee CN, Vincent AL. A COL17A1 Splice-Altering Mutation Is Prevalent in Inherited Recurrent Corneal Erosions. Ophthalmology 2016; 123:709-22. [PMID: 26786512 DOI: 10.1016/j.ophtha.2015.12.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 11/06/2015] [Accepted: 12/05/2015] [Indexed: 12/28/2022] Open
Abstract
PURPOSE Corneal dystrophies are a genetically heterogeneous group of disorders. We previously described a family with an autosomal dominant epithelial recurrent erosion dystrophy (ERED). We aimed to identify the underlying genetic cause of ERED in this family and 3 additional ERED families. We sought to characterize the potential function of the candidate genes using the human and zebrafish cornea. DESIGN Case series study of 4 white families with a similar ERED. An experimental study was performed on human and zebrafish tissue to examine the putative biological function of candidate genes. PARTICIPANTS Four ERED families, including 28 affected and 17 unaffected individuals. METHODS HumanLinkage-12 arrays (Illumina, San Diego, CA) were used to genotype 17 family members. Next-generation exome sequencing was performed on an uncle-niece pair. Segregation of potential causative mutations was confirmed using Sanger sequencing. Protein expression was determined using immunohistochemistry in human and zebrafish cornea. Gene expression in zebrafish was assessed using whole-mount in situ hybridization. Morpholino-induced transient gene knockdown was performed in zebrafish embryos. MAIN OUTCOME MEASURES Linkage microarray, exome analysis, DNA sequence analysis, immunohistochemistry, in situ hybridization, and morpholino-induced genetic knockdown results. RESULTS Linkage microarray analysis identified a candidate region on chromosome chr10:12,576,562-112,763,135, and exploration of exome sequencing data identified 8 putative pathogenic variants in this linkage region. Two variants segregated in 06NZ-TRB1 with ERED: COL17A1 c.3156C→T and DNAJC9 c.334G→A. The COL17A1 c.3156C→T variant segregated in all 4 ERED families. We showed biologically relevant expression of these proteins in human cornea. Both proteins are expressed in the cornea of zebrafish embryos and adults. Zebrafish lacking Col17a1a and Dnajc9 during development show no gross corneal phenotype. CONCLUSIONS The COL17A1 c.3156C→T variant is the likely causative mutation in our recurrent corneal erosion families, and its presence in 4 independent families suggests that it is prevalent in ERED. This same COL17A1 c.3156C→T variant recently was identified in a separate pedigree with ERED. Our study expands the phenotypic spectrum of COL17A1 disease from autosomal recessive epidermolysis bullosa to autosomal dominant ERED and identifies COL17A1 as a key protein in maintaining integrity of the corneal epithelium.
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Affiliation(s)
- Verity F Oliver
- Department of Ophthalmology, New Zealand National Eye Centre, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Katherine A van Bysterveldt
- Department of Ophthalmology, New Zealand National Eye Centre, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Murray Cadzow
- Department of Biochemistry, Dunedin School of Medicine, Otago University, Dunedin, New Zealand
| | - Bernhard Steger
- Department of Corneal and External Eye Diseases, St. Paul's Eye Unit, Royal Liverpool University Hospital, Liverpool, United Kingdom
| | - Vito Romano
- Department of Corneal and External Eye Diseases, St. Paul's Eye Unit, Royal Liverpool University Hospital, Liverpool, United Kingdom
| | - David Markie
- Pathology Department, Dunedin School of Medicine, Otago University, Dunedin, New Zealand
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia; Lions Eye Institute, University of Western Australia, Perth, Australia
| | - David A Mackey
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia; Lions Eye Institute, University of Western Australia, Perth, Australia
| | - Colin E Willoughby
- Department of Corneal and External Eye Diseases, St. Paul's Eye Unit, Royal Liverpool University Hospital, Liverpool, United Kingdom; Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
| | - Trevor Sherwin
- Department of Ophthalmology, New Zealand National Eye Centre, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Philip S Crosier
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Charles N McGhee
- Department of Ophthalmology, New Zealand National Eye Centre, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand; Eye Department, Greenlane Clinical Centre, Auckland District Health Board, Auckland, New Zealand
| | - Andrea L Vincent
- Department of Ophthalmology, New Zealand National Eye Centre, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand; Eye Department, Greenlane Clinical Centre, Auckland District Health Board, Auckland, New Zealand.
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Oda M, Kurogi M, Kubo Y, Saitoh O. Sensitivities of Two Zebrafish TRPA1 Paralogs to Chemical and Thermal Stimuli Analyzed in Heterologous Expression Systems. Chem Senses 2016; 41:261-72. [PMID: 26826723 DOI: 10.1093/chemse/bjv091] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/24/2015] [Indexed: 11/13/2022] Open
Abstract
Transient receptor potential A1 (TRPA1) is the only member of the mouse, chick, and frog TRPA family, whereas 2 paralogs (zTRPA1a and zTRPA1b) are present in zebrafish. We herein investigated functional differences in the 2 zebrafish TRPA1s. HEK293T cells were used as heterologous expression systems, and the sensitivities of these cells to 4 chemical irritants (allyl isothiocyanate [AITC], caffeine, auto-oxidized epigallocatechin gallate [EGCG], and hydrogen peroxide [H2O2]) were compared with Ca(2+) imaging techniques. Sensitivities to the activators for AITC, oxidized EGCG, and H2O2 were higher in cells expressing zTRPA1a than in those expressing zTRPA1b, whereas caffeine appeared to activate both cells equally. We also characterized the thermal sensitivity of Xenopus oocytes expressing each TRPA1 electrophysiologically using a 2-electrode voltage clamp. Although endogenous currents induced by a cold stimulation were observed in control oocytes in some batches, oocytes expressing zTRPA1b showed significantly stronger cold- and heat-induced responses. However, significant thermal activation was not observed in oocytes expressing zTRPA1a. The results obtained using in vitro expression systems suggest that zTRPA1a is specialized for chemical sensing, whereas zTRPA1b responds to thermal stimuli. Furthermore, characterization of the chimeric molecule of TRPA1a and 1b revealed the importance of the N-terminal region in chemical and thermal sensing by zTRPA1s.
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Affiliation(s)
- Mai Oda
- Department of Animal Bio-Science, Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama-shi, Shiga 526-0829, Japan
| | - Mako Kurogi
- Department of Animal Bio-Science, Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama-shi, Shiga 526-0829, Japan
| | - Yoshihiro Kubo
- Division of Biophysics and Neurobiology, Department of Molecular Physiology, National Institute for Physiological Sciences, Nishigohnaka38, Myodaiji, Okazaki, Aichi 444-8585, Japan and Department of Physiological Sciences, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama, Kanagawa 240-0155, Japan
| | - Osamu Saitoh
- Department of Animal Bio-Science, Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama-shi, Shiga 526-0829, Japan,
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113
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Tine M. Evolutionary significance and diversification of the phosphoglucose isomerase genes in vertebrates. BMC Res Notes 2015; 8:799. [PMID: 26682538 PMCID: PMC4684624 DOI: 10.1186/s13104-015-1683-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/09/2015] [Indexed: 01/20/2024] Open
Abstract
Background Phosphoglucose isomerase (PGI) genes are important multifunctional proteins whose evolution has, until now, not been well elucidated because of the limited number of completely sequenced genomes. Although the multifunctionality of this gene family has been considered as an original and innate characteristic, PGI genes may have acquired novel functions through changes in coding sequences and exon/intron structure, which are known to lead to functional divergence after gene duplication. A whole-genome comparative approach was used to estimate the rates of molecular evolution of this protein family. Results The results confirm the presence of two isoforms in teleost fishes and only one variant in all other vertebrates. Phylogenetic reconstructions grouped the PGI genes into five main groups: lungfishes/coelacanth/cartilaginous fishes, teleost fishes, amphibians, reptiles/birds and mammals, with the teleost group being subdivided into two subclades comprising PGI1 and PGI2. This PGI partitioning into groups is consistent with the synteny and molecular evolution results based on the estimation of the ratios of nonsynonymous to synonymous changes (Ka/Ks) and divergence rates between both PGI paralogs and orthologs. Teleost PGI2 shares more similarity with the variant found in all other vertebrates, suggesting that it has less evolved than PGI1 relative to the PGI of common vertebrate ancestor. Conclusions The diversification of PGI genes into PGI1 and PGI2 is consistent with a teleost-specific duplication before the radiation of this lineage, and after its split from the other infraclasses of ray-finned fishes. The low average Ka/Ks ratios within teleost and mammalian lineages suggest that both PGI1 and PGI2 are functionally constrained by purifying selection and may, therefore, have the same functions. By contrast, the high average Ka/Ks ratios and divergence rates within reptiles and birds indicate that PGI may be involved in different functions. The synteny analyses show that the genomic region harbouring PGI genes has independently undergone genomic rearrangements in mammals versus the reptile/bird lineage in particular, which may have contributed to the actual functional diversification of this gene family. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1683-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mbaye Tine
- Molecular Zoology Laboratory, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa. .,Genome Centre Cologne at MPI for Plant Breeding Research, 22 Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
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114
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Akhtar MT, Mushtaq MY, Verpoorte R, Richardson MK, Choi YH. Zebrafish as a Model for Systems Medicine R&D: Rethinking the Metabolic Effects of Carrier Solvents and Culture Buffers Determined by (1)H NMR Metabolomics. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 20:42-52. [PMID: 26669610 DOI: 10.1089/omi.2015.0119] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Zebrafish is a frequently employed model organism in systems medicine and biomarker discovery. A crosscutting fundamental question, and one that has been overlooked in the field, is the "system-wide" (omics) effects induced in zebrafish by metabolic solvents and culture buffers. Indeed, any bioactivity or toxicity test requires that the target compounds are dissolved in an appropriate nonpolar solvent or aqueous media. It is important to know whether the solvent or the buffer itself has an effect on the zebrafish model organism. We evaluated the effects of two organic carrier solvents used in research with zebrafish, as well as in drug screening: dimethyl sulfoxide (DMSO) and ethanol, and two commonly used aqueous buffers (egg water and Hank's balanced salt solution). The effects of three concentrations (0.01, 0.1, and 1%) of DMSO and ethanol were tested in the 5-day-old zebrafish embryo using proton nuclear magnetic resonance ((1)H NMR) based metabolomics. DMSO (1% and 0.1%, but not 0.01%) exposure significantly decreased the levels of adenosine triphosphate (ATP), betaine, alanine, histidine, lactate, acetate, and creatine (p < 0.05). By contrast, ethanol exposure did not alter the embryos' metabolome at any concentration tested. The two different aqueous media noted above impacted the zebrafish embryo metabolome as evidenced by changes in valine, alanine, lactate, acetate, betaine, glycine, glutamate, adenosine triphosphate, and histidine. These results show that DMSO has greater effects on the embryo metabolome than ethanol, and thus is used with caution as a carrier solvent in zebrafish biomarker research and oral medicine. Moreover, the DMSO concentration should not be higher than 0.01%. Careful attention is also warranted for the use of the buffers egg water and Hank's balanced salt solution in zebrafish. In conclusion, as zebrafish is widely used as a model organism in life sciences, metabolome changes induced by solvents and culture buffers warrant further attention for robust systems science, and precision biomarkers that will stand the test of time.
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Affiliation(s)
- Muhammad T Akhtar
- 1 Natural Products Laboratory, Leiden University , Leiden, the Netherlands .,3 Laboratory of Natural Products, Institute of Bioscience, University Putra Malaysia , Serdang, Malaysia
| | - Mian Y Mushtaq
- 1 Natural Products Laboratory, Leiden University , Leiden, the Netherlands .,4 Department of Pharmaceutical Chemistry, Faculty of Pharmacy, International Islamic University , Kuantan, Malaysia
| | - Robert Verpoorte
- 1 Natural Products Laboratory, Leiden University , Leiden, the Netherlands
| | - Michael K Richardson
- 2 Sylvius Laboratory, Institute of Biology, Leiden University , Leiden, the Netherlands
| | - Young H Choi
- 1 Natural Products Laboratory, Leiden University , Leiden, the Netherlands
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115
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Walter RB, Obara T. Workshop report: The medaka model for comparative assessment of human disease mechanisms. Comp Biochem Physiol C Toxicol Pharmacol 2015; 178:156-162. [PMID: 26099189 PMCID: PMC4662895 DOI: 10.1016/j.cbpc.2015.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/08/2015] [Accepted: 06/09/2015] [Indexed: 11/29/2022]
Abstract
Results of recent studies showing the utility of medaka as a model of various human disease states were presented at the 7th Aquatic Models of Human Disease Conference (December 13-18, 2014, Austin, TX). This conference brought together many of the most highly regarded national and international scientists that employ the medaka model in their investigations. To take advantage of this opportunity, a cohort of established medaka researchers were asked to stay an extra day and represent the medaka scientific community in a workshop entitled "The Medaka Model for Comparative Assessment of Human Disease Mechanisms." The central purpose of this medaka workshop was to assess current use and project the future resource needs of the American medaka research community. The workshop sought to spur discussions of issues that would promote more informative comparative disease model studies. Finally, workshop attendees met together to propose, discuss, and agree on recommendations regarding the most effective research resources needed to enable US scientists to perform experiments leading to impacting experimental results that directly translate to human disease. Consistent with this central purpose, the workshop was divided into two sessions of invited speakers having expertise and experience in the session topics. The workshop hosted 20 scientific participants (Appendices 1 and 2), and of these, nine scientists presented formal talks. Here, we present a summary report stemming from workshop presentations and subsequent round table discussions and forward recommendations from this group that we believe represent views of the overall medaka research community.
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Affiliation(s)
- Ronald B Walter
- Department of Chemistry and Biochemistry, Xiphophorus Genetic Stock Center, Texas State University, 419 Centennial Hall, San Marcos, TX 78666, USA.
| | - Tomoko Obara
- Department of Cell Biology, University of Oklahoma Health Sciences Center, BRC Room 256, 975 N.E. 10th St., Oklahoma City, OK 73104-5419, USA.
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116
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Bain PA, Papanicolaou A, Kumar A. Identification of Putative Nuclear Receptors and Steroidogenic Enzymes in Murray-Darling Rainbowfish (Melanotaenia fluviatilis) Using RNA-Seq and De Novo Transcriptome Assembly. PLoS One 2015; 10:e0142636. [PMID: 26599404 PMCID: PMC4658143 DOI: 10.1371/journal.pone.0142636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/23/2015] [Indexed: 11/18/2022] Open
Abstract
Murray-Darling rainbowfish (Melanotaenia fluviatilis [Castelnau, 1878]; Atheriniformes: Melanotaeniidae) is a small-bodied teleost currently under development in Australasia as a test species for aquatic toxicological studies. To date, efforts towards the development of molecular biomarkers of contaminant exposure have been hindered by the lack of available sequence data. To address this, we sequenced messenger RNA from brain, liver and gonads of mature male and female fish and generated a high-quality draft transcriptome using a de novo assembly approach. 149,742 clusters of putative transcripts were obtained, encompassing 43,841 non-redundant protein-coding regions. Deduced amino acid sequences were annotated by functional inference based on similarity with sequences from manually curated protein sequence databases. The draft assembly contained protein-coding regions homologous to 95.7% of the complete cohort of predicted proteins from the taxonomically related species, Oryzias latipes (Japanese medaka). The mean length of rainbowfish protein-coding sequences relative to their medaka homologues was 92.1%, indicating that despite the limited number of tissues sampled a large proportion of the total expected number of protein-coding genes was captured in the study. Because of our interest in the effects of environmental contaminants on endocrine pathways, we manually curated subsets of coding regions for putative nuclear receptors and steroidogenic enzymes in the rainbowfish transcriptome, revealing 61 candidate nuclear receptors encompassing all known subfamilies, and 41 putative steroidogenic enzymes representing all major steroidogenic enzymes occurring in teleosts. The transcriptome presented here will be a valuable resource for researchers interested in biomarker development, protein structure and function, and contaminant-response genomics in Murray-Darling rainbowfish.
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Affiliation(s)
- Peter A. Bain
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Division of Land and Water, Urrbrae, South Australia, Australia
- * E-mail:
| | - Alexie Papanicolaou
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Division of Land and Water, Black Mountain, Australian Capital Territory, Australia
| | - Anupama Kumar
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Division of Land and Water, Urrbrae, South Australia, Australia
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117
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Wang L, Wan ZY, Bai B, Huang SQ, Chua E, Lee M, Pang HY, Wen YF, Liu P, Liu F, Sun F, Lin G, Ye BQ, Yue GH. Construction of a high-density linkage map and fine mapping of QTL for growth in Asian seabass. Sci Rep 2015; 5:16358. [PMID: 26553309 PMCID: PMC4639833 DOI: 10.1038/srep16358] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/01/2015] [Indexed: 01/06/2023] Open
Abstract
A high-density genetic map is essential for comparative genomic studies and fine mapping of QTL, and can also facilitate genome sequence assembly. Here, a high density genetic map of Asian seabass was constructed with 3321 SNPs generated by sequencing 144 individuals in a F2 family. The length of the map was 1577.67 cM with an average marker interval of 0.52 cM. A high level of genomic synteny among Asian seabass, European seabass, Nile tilapia and stickleback was detected. Using this map, one genome-wide significant and five suggestive QTL for growth traits were detected in six linkage groups (i.e. LG4, LG5, LG11, LG13, LG14 and LG15). These QTL explained 10.5–16.0% of phenotypic variance. A candidate gene, ACOX1 within the significant QTL on LG5 was identified. The gene was differentially expressed between fast- and slow-growing Asian seabass. The high-density SNP-based map provides an important tool for fine mapping QTL in molecular breeding and comparative genome analysis.
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Affiliation(s)
- Le Wang
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Zi Yi Wan
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Bin Bai
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Shu Qing Huang
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Elaine Chua
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - May Lee
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Hong Yan Pang
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Yan Fei Wen
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Peng Liu
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Feng Liu
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Fei Sun
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Grace Lin
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Bao Qing Ye
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Gen Hua Yue
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604.,Department of Biological Sciences, National University of Singapore, 14 Science Drive, Singapore 117543.,School of Biological Sciences, Nanyang Technological University, 6 Nanyang Drive, Singapore 637551
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Abstract
The formation of the face and skull involves a complex series of developmental events mediated by cells derived from the neural crest, endoderm, mesoderm, and ectoderm. Although vertebrates boast an enormous diversity of adult facial morphologies, the fundamental signaling pathways and cellular events that sculpt the nascent craniofacial skeleton in the embryo have proven to be highly conserved from fish to man. The zebrafish Danio rerio, a small freshwater cyprinid fish from eastern India, has served as a popular model of craniofacial development since the 1990s. Unique strengths of the zebrafish model include a simplified skeleton during larval stages, access to rapidly developing embryos for live imaging, and amenability to transgenesis and complex genetics. In this chapter, we describe the anatomy of the zebrafish craniofacial skeleton; its applications as models for the mammalian jaw, middle ear, palate, and cranial sutures; the superior imaging technology available in fish that has provided unprecedented insights into the dynamics of facial morphogenesis; the use of the zebrafish to decipher the genetic underpinnings of craniofacial biology; and finally a glimpse into the most promising future applications of zebrafish craniofacial research.
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119
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Acute caffeine administration affects zebrafish response to a robotic stimulus. Behav Brain Res 2015; 289:48-54. [DOI: 10.1016/j.bbr.2015.04.020] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Revised: 04/08/2015] [Accepted: 04/11/2015] [Indexed: 11/22/2022]
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120
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Samenkova NF, Kisrieva YS, Petushkova NA, Kuznetsova GP, Larina OV, Trifonova OP, Karuzina II, Ipatova OM, Lisitsa AV. [Analysis of proteomic profile changes of zebrafish embryos during exposure to doxorubicin, built-in the phospholipid transport nanosystem]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2015. [PMID: 26215412 DOI: 10.18097/pbmc20156103350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The proteome profile of Danio rerio embryos grown in the medium containing doxorubicin, included in the phospholipid transport nanosystem (doxolip) has been investigated using combination of 1D-electrophoresis with subsequent MALDI-TOF-PMF mass spectrometry. Cultivation of growing of D. rerio embryos in the medium with doxolip caused a substantial increase in expression of the cytoskeletal proteins, a decrease in the number of nuclear proteins involved in DNA and RNA synthesis and disappearance of vitellogenin 2 in comparison with control (the cultivation medium containing the phospholipid transport nanosystem). Analysis of the proteomic profiles of doxolip-treated embryos suggests lower toxicity of doxorubicin incorporated in the phospholipid nanosystem.
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Affiliation(s)
| | - Y S Kisrieva
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | - O V Larina
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - I I Karuzina
- Institute of Biomedical Chemistry, Moscow, Russia
| | - O M Ipatova
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A V Lisitsa
- Institute of Biomedical Chemistry, Moscow, Russia
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121
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Bishop B, Ho KK, Tyler K, Smith A, Bonilla S, Leung YF, Ogas J. The chromatin remodeler chd5 is necessary for proper head development during embryogenesis of Danio rerio. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1040-50. [PMID: 26092436 DOI: 10.1016/j.bbagrm.2015.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 06/05/2015] [Accepted: 06/12/2015] [Indexed: 12/12/2022]
Abstract
The chromatin remodeler CHD5 plays a critical role in tumor suppression and neurogenesis in mammals. CHD5 contributes to gene expression during neurogenesis, but there is still much to learn regarding how this class of remodelers contributes to differentiation and development. CHD5 remodelers are vertebrate-specific, raising the prospect that CHD5 plays one or more conserved roles in this phylum. Expression of chd5 in adult fish closely mirrors expression of CHD5 in adult mammals. Knockdown of Chd5 during embryogenesis suggests new roles for CHD5 remodelers based on resulting defects in craniofacial development including reduced head and eye size as well as reduced cartilage formation in the head. In addition, knockdown of Chd5 results in altered expression of neural markers in the developing brain and eye as well as a profound defect in differentiation of dopaminergic amacrine cells. Recombinant zebrafish Chd5 protein exhibits nucleosome remodeling activity in vitro, suggesting that it is the loss of this activity that contributes to the observed phenotypes. Our studies indicate that zebrafish is an appropriate model for functional characterization of CHD5 remodelers in vertebrates and highlight the potential of this model for generating novel insights into the role of this vital class of remodelers.
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Affiliation(s)
- Brett Bishop
- Department of Biochemistry and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, United States
| | - Kwok Ki Ho
- Department of Biochemistry and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, United States
| | - Kim Tyler
- Department of Biochemistry and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, United States
| | - Amanda Smith
- Department of Biochemistry and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, United States
| | - Sylvia Bonilla
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, United States
| | - Yuk Fai Leung
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, United States
| | - Joe Ogas
- Department of Biochemistry and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, United States.
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122
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Luzio A, Coimbra AM, Benito C, Fontaínhas-Fernandes AA, Matos M. Screening and identification of potential sex-associated sequences in Danio rerio. Mol Reprod Dev 2015; 82:756-64. [PMID: 26013562 DOI: 10.1002/mrd.22508] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 05/18/2015] [Indexed: 02/02/2023]
Abstract
Current knowledge on zebrafish (Danio rerio) suggests that sex determination has a polygenic genetic basis in this species, although environmental factors may also be involved. This study aimed to identify sex-associated genomic regions using two different marker systems: inter-simple sequence repeats (ISSRs) and random-amplified polymorphic DNA (RAPDs). Two bulks were constructed: one with DNA from zebrafish females and the other from males; then, a total of 100 ISSR and 280 RAPD primers were tested. Three DNA fragments presenting sexual dimorphism (female-linked: OPA17436 and OPQ191027 ; male-linked: OPQ19951 ) were determined from sequential analysis of the bulks followed by assessment in individuals. These fragments were cloned and convert into the following sequenced characterized amplified regions (SCAR): DrSM_F1, DrSM_F2, and DrSM_M, which share identities with sequences located in chromosomes 2, 3, and 11 (Zv9), respectively. Using these potential markers in zebrafish samples it was possible to correctly identify 80% of the males (DrSM_M) and 100% of the females (DrSM_F1 + DrSM_F2) in the analyzed population.
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Affiliation(s)
- Ana Luzio
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, CITAB, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - Ana M Coimbra
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, CITAB, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - César Benito
- Departamento de Genética, Facultad de Biologia, Universidad Complutense, Madrid, Spain
| | - António A Fontaínhas-Fernandes
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, CITAB, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - Manuela Matos
- Departamento de Genética e Biotecnologia (DGB), Escola de Ciências da Vida e do Ambiente (ECVA), Universidade de Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
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123
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Gout JF, Lynch M. Maintenance and Loss of Duplicated Genes by Dosage Subfunctionalization. Mol Biol Evol 2015; 32:2141-8. [PMID: 25908670 DOI: 10.1093/molbev/msv095] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Whole-genome duplications (WGDs) have contributed to gene-repertoire enrichment in many eukaryotic lineages. However, most duplicated genes are eventually lost and it is still unclear why some duplicated genes are evolutionary successful whereas others quickly turn to pseudogenes. Here, we show that dosage constraints are major factors opposing post-WGD gene loss in several Paramecium species that share a common ancestral WGD. We propose a model where a majority of WGD-derived duplicates preserve their ancestral function and are retained to produce enough of the proteins performing this same ancestral function. Under this model, the expression level of individual duplicated genes can evolve neutrally as long as they maintain a roughly constant summed expression, and this allows random genetic drift toward uneven contributions of the two copies to total expression. Our analysis suggests that once a high level of imbalance is reached, which can require substantial lengths of time, the copy with the lowest expression level contributes a small enough fraction of the total expression that selection no longer opposes its loss. Extension of our analysis to yeast species sharing a common ancestral WGD yields similar results, suggesting that duplicated-gene retention for dosage constraints followed by divergence in expression level and eventual deterministic gene loss might be a universal feature of post-WGD evolution.
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Affiliation(s)
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington
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124
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A Multifunctional Mutagenesis System for Analysis of Gene Function in Zebrafish. G3-GENES GENOMES GENETICS 2015; 5:1283-99. [PMID: 25840430 PMCID: PMC4478556 DOI: 10.1534/g3.114.015842] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Since the sequencing of the human reference genome, many human disease-related genes have been discovered. However, understanding the functions of all the genes in the genome remains a challenge. The biological activities of these genes are usually investigated in model organisms such as mice and zebrafish. Large-scale mutagenesis screens to generate disruptive mutations are useful for identifying and understanding the activities of genes. Here, we report a multifunctional mutagenesis system in zebrafish using the maize Ds transposon. Integration of the Ds transposable element containing an mCherry reporter for protein trap events and an EGFP reporter for enhancer trap events produced a collection of transgenic lines marking distinct cell and tissue types, and mutagenized genes in the zebrafish genome by trapping and prematurely terminating endogenous protein coding sequences. We obtained 642 zebrafish lines with dynamic reporter gene expression. The characterized fish lines with specific expression patterns will be made available through the European Zebrafish Resource Center (EZRC), and a database of reporter expression is available online (http://fishtrap.warwick.ac.uk/). Our approach complements other efforts using zebrafish to facilitate functional genomic studies in this model of human development and disease.
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125
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Hertel J, Stadler PF. The Expansion of Animal MicroRNA Families Revisited. Life (Basel) 2015; 5:905-20. [PMID: 25780960 PMCID: PMC4390885 DOI: 10.3390/life5010905] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/09/2015] [Accepted: 02/11/2015] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs are important regulatory small RNAs in many eukaryotes. Due to their small size and simple structure, they are readily innovated de novo. Throughout the evolution of animals, the emergence of novel microRNA families traces key morphological innovations. Here, we use a computational approach based on homology search and parsimony-based presence/absence analysis to draw a comprehensive picture of microRNA evolution in 159 animal species. We confirm previous observations regarding bursts of innovations accompanying the three rounds of genome duplications in vertebrate evolution and in the early evolution of placental mammals. With a much better resolution for the invertebrate lineage compared to large-scale studies, we observe additional bursts of innovation, e.g., in Rhabditoidea. More importantly, we see clear evidence that loss of microRNA families is not an uncommon phenomenon. The Enoplea may serve as a second dramatic example beyond the tunicates. The large-scale analysis presented here also highlights several generic technical issues in the analysis of very large gene families that will require further research.
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Affiliation(s)
- Jana Hertel
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5E, 04103 Leipzig, Germany.
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany.
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, D-04103 Leipzig, Germany.
- Department of Theoretical Chemistry of the University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria.
- Center for RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, Frederiksberg C, Denmark.
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA.
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126
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Shao C, Niu Y, Rastas P, Liu Y, Xie Z, Li H, Wang L, Jiang Y, Tai S, Tian Y, Sakamoto T, Chen S. Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis. DNA Res 2015; 22:161-70. [PMID: 25762582 PMCID: PMC4401326 DOI: 10.1093/dnares/dsv001] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 02/01/2015] [Indexed: 12/18/2022] Open
Abstract
High-resolution genetic maps are essential for fine mapping of complex traits, genome assembly, and comparative genomic analysis. Single-nucleotide polymorphisms (SNPs) are the primary molecular markers used for genetic map construction. In this study, we identified 13,362 SNPs evenly distributed across the Japanese flounder (Paralichthys olivaceus) genome. Of these SNPs, 12,712 high-confidence SNPs were subjected to high-throughput genotyping and assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 3,497.29 cM with an average distance of 0.47 cM between loci, thereby representing the densest genetic map currently reported for Japanese flounder. Nine positive quantitative trait loci (QTLs) forming two main clusters for Vibrio anguillarum disease resistance were detected. All QTLs could explain 5.1-8.38% of the total phenotypic variation. Synteny analysis of the QTL regions on the genome assembly revealed 12 immune-related genes, among them 4 genes strongly associated with V. anguillarum disease resistance. In addition, 246 genome assembly scaffolds with an average size of 21.79 Mb were anchored onto the LGs; these scaffolds, comprising 522.99 Mb, represented 95.78% of assembled genomic sequences. The mapped assembly scaffolds in Japanese flounder were used for genome synteny analyses against zebrafish (Danio rerio) and medaka (Oryzias latipes). Flounder and medaka were found to possess almost one-to-one synteny, whereas flounder and zebrafish exhibited a multi-syntenic correspondence. The newly developed high-resolution genetic map, which will facilitate QTL mapping, scaffold assembly, and genome synteny analysis of Japanese flounder, marks a milestone in the ongoing genome project for this species.
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Affiliation(s)
- Changwei Shao
- Ministry of Agriculture, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao 266071, China Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao 266071, China Faculty of Marine Science, Tokyo University of Marine Science and Technology, Minato, Tokyo 108-8477, Japan
| | | | - Pasi Rastas
- Department of Biosciences, Metapopulation Research Group, University of Helsinki, Helsinki FI-00014, Finland
| | - Yang Liu
- Ministry of Agriculture, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao 266071, China Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao 266071, China
| | | | - Hengde Li
- Chinese Academy of Fisheries Science, Beijing 100039, China
| | - Lei Wang
- Ministry of Agriculture, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao 266071, China Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao 266071, China
| | - Yong Jiang
- National Oceanographic Center, Qingdao 266071, China
| | | | - Yongsheng Tian
- Ministry of Agriculture, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao 266071, China Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao 266071, China
| | - Takashi Sakamoto
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, Minato, Tokyo 108-8477, Japan
| | - Songlin Chen
- Ministry of Agriculture, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao 266071, China Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao 266071, China
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127
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Farré M, Robinson TJ, Ruiz-Herrera A. An Integrative Breakage Model of genome architecture, reshuffling and evolution: The Integrative Breakage Model of genome evolution, a novel multidisciplinary hypothesis for the study of genome plasticity. Bioessays 2015; 37:479-88. [PMID: 25739389 DOI: 10.1002/bies.201400174] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 12/23/2022]
Abstract
Our understanding of genomic reorganization, the mechanics of genomic transmission to offspring during germ line formation, and how these structural changes contribute to the speciation process, and genetic disease is far from complete. Earlier attempts to understand the mechanism(s) and constraints that govern genome remodeling suffered from being too narrowly focused, and failed to provide a unified and encompassing view of how genomes are organized and regulated inside cells. Here, we propose a new multidisciplinary Integrative Breakage Model for the study of genome evolution. The analysis of the high-level structural organization of genomes (nucleome), together with the functional constrains that accompany genome reshuffling, provide insights into the origin and plasticity of genome organization that may assist with the detection and isolation of therapeutic targets for the treatment of complex human disorders.
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Affiliation(s)
- Marta Farré
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Campus UAB, Barcelona, Spain
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128
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Teixidó E, Piqué E, Gonzalez-Linares J, Llobet JM, Gómez-Catalán J. Developmental effects and genotoxicity of 10 water disinfection by-products in zebrafish. JOURNAL OF WATER AND HEALTH 2015; 13:54-66. [PMID: 25719465 DOI: 10.2166/wh.2014.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Disinfection by-products are contaminants produced during drinking water disinfection. Several DBPs have been implicated in a variety of toxic effects, mainly carcinogenic and genotoxic effects. Moreover, DBPs exposure has also been associated with an increased risk of developmental effects. In this study, the developmental toxicity and genotoxicity of 10 DBPs (four trihalomethanes [THMs], five haloacetic acids [HAAs] and sodium bromate) in the zebrafish embryo model were evaluated. Embryos exposed for 72 hours were observed for different endpoints such as growth, hatching success, malformations and lethality. THMs exposure resulted in adverse developmental effects and a significant reduced tail length. Two HAAs, tribromoacetic acid and dichloroacetic acid, along with sodium bromate were found to cause a significant increase in malformation rate. Chloroform, chlorodibromomethane and sodium bromate produced a weak induction of DNA damage to whole embryos. However, developmental effects occurred at a range of concentrations (20-100 μg/mL) several orders of magnitude above the levels that can be attained in fetal blood in humans exposed to chlorinated water. In conclusion, the teratogenic and genotoxic activity observed by some DBPs in zebrafish reinforce the view that there is a weak capacity of disinfection products to cause developmental effects at environmentally relevant concentrations.
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Affiliation(s)
- Elisabet Teixidó
- GRET-CERETOX and Toxicology Unit, Public Health Department, School of Pharmacy, University of Barcelona. Av. Joan XXIII s/n, E-08028, Barcelona, Spain E-mail:
| | - Esther Piqué
- GRET-CERETOX and Toxicology Unit, Public Health Department, School of Pharmacy, University of Barcelona. Av. Joan XXIII s/n, E-08028, Barcelona, Spain E-mail:
| | - Javier Gonzalez-Linares
- GRET-CERETOX and Experimental Toxicology and Ecotoxicology Unit, Barcelona Science Park. Baldiri i Reixac 10-12, E-08028, Barcelona, Spain
| | - Joan M Llobet
- GRET-CERETOX and Toxicology Unit, Public Health Department, School of Pharmacy, University of Barcelona. Av. Joan XXIII s/n, E-08028, Barcelona, Spain E-mail:
| | - Jesús Gómez-Catalán
- GRET-CERETOX and Toxicology Unit, Public Health Department, School of Pharmacy, University of Barcelona. Av. Joan XXIII s/n, E-08028, Barcelona, Spain E-mail:
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129
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Comparative mapping for bighead carp (Aristichthys nobilis) against model and non-model fishes provides insights into the genomic evolution of cyprinids. Mol Genet Genomics 2015; 290:1313-26. [PMID: 25627158 DOI: 10.1007/s00438-015-0992-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 01/09/2015] [Indexed: 02/03/2023]
Abstract
Comparative mapping provides an efficient method to connect genomes of non-model and model fishes. In this study, we used flanking sequences of the 659 microsatellites on a genetic map of bighead carp (Aristichthys nobilis) to comprehensively study syntenic relationships between bighead carp and nine model and non-model fishes. Of the five model and two food fishes with whole genome data, Cyprinus carpio showed the highest rate of positive BLAST hits (95.3 %) with bighead carp map, followed by Danio rerio (70.9 %), Oreochromis niloticus (21.7 %), Tetraodon nigroviridis (6.4 %), Gasterosteus aculeatus (5.2 %), Oryzias latipes (4.7 %) and Fugu rubripes (3.5 %). Chromosomal syntenic analyses showed that inversion was the basic chromosomal rearrangement during genomic evolution of cyprinids, and the extent of inversions and translocations was found to be positively correlated with evolutionary relationships among fishes studied. Among the five investigated cyprinids, linkage groups (LGs) of bighead carp, Hypophthalmichthys molitrix and Ctenopharyngodon idella exhibited a one-to-one relationship. Besides, LG 9 of bighead carp and homologous LGs of silver carp and grass carp all corresponded to the chromosomes 10 and 22 of zebrafish, suggesting that chromosomal fission may have occurred in the ancestor of zebrafish. On the other hand, LGs of bighead carp and common carp showed an approximate one-to-two relationship with extensive translocations, confirming the occurrence of a 4th whole genome duplication in common carp. This study provides insights into the understanding of genome evolution among cyprinids and would aid in transferring positional and functional information of genes from model fish like zebrafish to non-model fish like bighead carp.
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130
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Oosterhof N, Boddeke E, van Ham TJ. Immune cell dynamics in the CNS: Learning from the zebrafish. Glia 2014; 63:719-35. [PMID: 25557007 DOI: 10.1002/glia.22780] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 12/10/2014] [Indexed: 12/22/2022]
Abstract
A major question in research on immune responses in the brain is how the timing and nature of these responses influence physiology, pathogenesis or recovery from pathogenic processes. Proper understanding of the immune regulation of the human brain requires a detailed description of the function and activities of the immune cells in the brain. Zebrafish larvae allow long-term, noninvasive imaging inside the brain at high-spatiotemporal resolution using fluorescent transgenic reporters labeling specific cell populations. Together with recent additional technical advances this allows an unprecedented versatility and scope of future studies. Modeling of human physiology and pathology in zebrafish has already yielded relevant insights into cellular dynamics and function that can be translated to the human clinical situation. For instance, in vivo studies in the zebrafish have provided new insight into immune cell dynamics in granuloma formation in tuberculosis and the mechanisms involving treatment resistance. In this review, we highlight recent findings and novel tools paving the way for basic neuroimmunology research in the zebrafish. GLIA 2015;63:719-735.
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Affiliation(s)
- Nynke Oosterhof
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
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131
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An LH, Zheng BH, Liu RZ, Fan Q, Wang QK, Luo YF. Transcriptomic response to estrogen exposure in the male Zhikong scallop, Chlamys farreri. MARINE POLLUTION BULLETIN 2014; 89:59-66. [PMID: 25455372 DOI: 10.1016/j.marpolbul.2014.10.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 10/10/2014] [Accepted: 10/16/2014] [Indexed: 06/04/2023]
Abstract
The transcriptomes of Zhikong scallop exposed to 17β-estradiol were determined using the Roche/454. A total of 51,997 unigenes, representing 45,030 contigs and 6967 singlets were obtained. And 14,028, 19,798 and 14,981 of these unigenes were annotated from the non-redundant nucleic acid database, non-redundant protein database and Swiss protein database, respectively. A total of 10,699 unigenes were further annotated to biological processes (9080), molecular functions (8692) and cellular components (7829) using the GO, and 8945 unigenes were mapped to biological pathways including the metabolism (2862) and genetic information processing (2263). Most importantly, 16,692 unigenes and 18,686 unigenes in testis, and 10,492 unigenes and 13,186 unigenes in digestive gland were up-regulated significantly after exposure to 50 and 500 ng E2/L; while 10,212 unigenes and 9409 unigenes in testis and 10,629 unigenes and 9463 unigenes in digestive gland were down-regulated. These valuable information provides insights into the mechanisms in invertebrate exposure to EDCs.
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Affiliation(s)
- Li-Hui An
- State Environmental Protection Key Laboratory of Estuarine and Coastal Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Bing-Hui Zheng
- State Environmental Protection Key Laboratory of Estuarine and Coastal Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Rui-Zhi Liu
- State Environmental Protection Key Laboratory of Estuarine and Coastal Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Qiang Fan
- State Environmental Protection Key Laboratory of Estuarine and Coastal Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Tianjin Agricultural College, Tianjin 300384, China
| | | | - Ying-Feng Luo
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
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132
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The circadian clock of teleost fish: a comparative analysis reveals distinct fates for duplicated genes. J Mol Evol 2014; 80:57-64. [PMID: 25487517 DOI: 10.1007/s00239-014-9660-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 11/26/2014] [Indexed: 10/24/2022]
Abstract
The circadian clock is a central oscillator that coordinates endogenous rhythms. Members of six gene families underlie the metabolic machinery of this system. Although this machinery appears to correspond to a highly conserved genetic system in metazoans, it has been recognized that vertebrates possess a more diverse gene inventory than that of non-vertebrates. This difference could have originated in the two successive rounds of whole-genome duplications that took place in the common ancestor of the group. Teleost fish underwent an extra event of whole-genome duplication, which is thought to have provided an abundance of raw genetic material for the biological innovations that facilitated the radiation of the group. In this study, we assessed the relative contributions of whole-genome duplication and small-scale gene duplication to generate the repertoire of genes associated with the circadian clock of teleost fish. To achieve this goal, we annotated genes from six gene families associated with the circadian clock in eight teleost fish species, and we reconstructed their evolutionary history by inferring phylogenetic relationships. Our comparative analysis indicated that teleost species possess a variable repertoire of genes related to the circadian clock gene families and that the actual diversity of these genes has been shaped by a variety of phenomena, such as the complete deletion of ohnologs, the differential retention of genes, and lineage-specific gene duplications. From a functional perspective, the subfunctionalization of two ohnolog genes (PER1a and PER1b) in zebrafish highlights the power of whole-genome duplications to generate biological diversity.
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133
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Garbarino G, Costa S, Pestarino M, Candiani S. Differential expression of synapsin genes during early zebrafish development. Neuroscience 2014; 280:351-67. [DOI: 10.1016/j.neuroscience.2014.09.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 09/03/2014] [Accepted: 09/03/2014] [Indexed: 11/27/2022]
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134
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Abstract
Sex determination can be robustly genetic, strongly environmental, or genetic subject to environmental perturbation. The genetic basis of sex determination is unknown for zebrafish (Danio rerio), a model for development and human health. We used RAD-tag population genomics to identify sex-linked polymorphisms. After verifying this "RAD-sex" method on medaka (Oryzias latipes), we studied two domesticated zebrafish strains (AB and TU), two natural laboratory strains (WIK and EKW), and two recent isolates from nature (NA and CB). All four natural strains had a single sex-linked region at the right tip of chromosome 4, enabling sex genotyping by PCR. Genotypes for the single nucleotide polymorphism (SNP) with the strongest statistical association to sex suggested that wild zebrafish have WZ/ZZ sex chromosomes. In natural strains, "male genotypes" became males and some "female genotypes" also became males, suggesting that the environment or genetic background can cause female-to-male sex reversal. Surprisingly, TU and AB lacked detectable sex-linked loci. Phylogenomics rooted on D. nigrofasciatus verified that all strains are monophyletic. Because AB and TU branched as a monophyletic clade, we could not rule out shared loss of the wild sex locus in a common ancestor despite their independent domestication. Mitochondrial DNA sequences showed that investigated strains represent only one of the three identified zebrafish haplogroups. Results suggest that zebrafish in nature possess a WZ/ZZ sex-determination mechanism with a major determinant lying near the right telomere of chromosome 4 that was modified during domestication. Strains providing the zebrafish reference genome lack key components of the natural sex-determination system but may have evolved variant sex-determining mechanisms during two decades in laboratory culture.
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135
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Feldman B, Tuchman M, Caldovic L. A zebrafish model of hyperammonemia. Mol Genet Metab 2014; 113:142-7. [PMID: 25069822 PMCID: PMC4191821 DOI: 10.1016/j.ymgme.2014.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 07/01/2014] [Accepted: 07/01/2014] [Indexed: 02/08/2023]
Abstract
Hyperammonemia is the principal consequence of urea cycle defects and liver failure, and the exposure of the brain to elevated ammonia concentrations leads to a wide range of neuro-cognitive deficits, intellectual disabilities, coma and death. Current treatments focus almost exclusively on either reducing ammonia levels through the activation of alternative pathways for ammonia disposal or on liver transplantation. Ammonia is toxic to most fish and its pathophysiology appears to be similar to that in mammals. Since hyperammonemia can be induced in fish simply by immersing them in water with elevated concentration of ammonia, we sought to develop a zebrafish (Danio rerio) model of hyperammonemia. When exposed to 3mM ammonium acetate (NH4Ac), 50% of 4-day old (dpf) fish died within 3hours and 4mM NH4Ac was 100% lethal. We used 4dpf zebrafish exposed to 4mM NH4Ac to test whether the glutamine synthetase inhibitor methionine sulfoximine (MSO) and/or NMDA receptor antagonists MK-801, memantine and ketamine, which are known to protect the mammalian brain from hyperammonemia, prolong survival of hyperammonemic fish. MSO, MK-801, memantine and ketamine all prolonged the lives of the ammonia-treated fish. Treatment with the combination of MSO and an NMDA receptor antagonist was more effective than either drug alone. These results suggest that zebrafish can be used to screen for ammonia-neuroprotective agents. If successful, drugs that are discovered in this screen could complement current treatment approaches to improve the outcome of patients with hyperammonemia.
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Affiliation(s)
- B Feldman
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - M Tuchman
- Children's National Medical Center, Washington DC, USA
| | - L Caldovic
- Children's National Medical Center, Washington DC, USA.
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136
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Glasauer SMK, Neuhauss SCF. Whole-genome duplication in teleost fishes and its evolutionary consequences. Mol Genet Genomics 2014; 289:1045-60. [PMID: 25092473 DOI: 10.1007/s00438-014-0889-2] [Citation(s) in RCA: 509] [Impact Index Per Article: 50.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 07/15/2014] [Indexed: 12/18/2022]
Abstract
Whole-genome duplication (WGD) events have shaped the history of many evolutionary lineages. One such duplication has been implicated in the evolution of teleost fishes, by far the most species-rich vertebrate clade. After initial controversy, there is now solid evidence that such event took place in the common ancestor of all extant teleosts. It is termed teleost-specific (TS) WGD. After WGD, duplicate genes have different fates. The most likely outcome is non-functionalization of one duplicate gene due to the lack of selective constraint on preserving both. Mechanisms that act on preservation of duplicates are subfunctionalization (partitioning of ancestral gene functions on the duplicates), neofunctionalization (assigning a novel function to one of the duplicates) and dosage selection (preserving genes to maintain dosage balance between interconnected components). Since the frequency of these mechanisms is influenced by the genes' properties, there are over-retained classes of genes, such as highly expressed ones and genes involved in neural function. The consequences of the TS-WGD, especially its impact on the massive radiation of teleosts, have been matter of controversial debate. It is evident that gene duplications are crucial for generating complexity and that WGDs provide large amounts of raw material for evolutionary adaptation and innovation. However, it is less clear whether the TS-WGD is directly linked to the evolutionary success of teleosts and their radiation. Recent studies let us conclude that TS-WGD has been important in generating teleost complexity, but that more recent ecological adaptations only marginally related to TS-WGD might have even contributed more to diversification. It is likely, however, that TS-WGD provided teleosts with diversification potential that can become effective much later, such as during phases of environmental change.
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Affiliation(s)
- Stella M K Glasauer
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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137
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McGrath CL, Gout JF, Johri P, Doak TG, Lynch M. Differential retention and divergent resolution of duplicate genes following whole-genome duplication. Genome Res 2014; 24:1665-75. [PMID: 25085612 PMCID: PMC4199370 DOI: 10.1101/gr.173740.114] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Paramecium aurelia complex is a group of 15 species that share at least three past whole-genome duplications (WGDs). The macronuclear genome sequences of P. biaurelia and P. sexaurelia are presented and compared to the published sequence of P. tetraurelia. Levels of duplicate-gene retention from the recent WGD differ by >10% across species, with P. sexaurelia losing significantly more genes than P. biaurelia or P. tetraurelia. In addition, historically high rates of gene conversion have homogenized WGD paralogs, probably extending the paralogs’ lifetimes. The probability of duplicate retention is positively correlated with GC content and expression level; ribosomal proteins, transcription factors, and intracellular signaling proteins are overrepresented among maintained duplicates. Finally, multiple sources of evidence indicate that P. sexaurelia diverged from the two other lineages immediately following, or perhaps concurrent with, the recent WGD, with approximately half of gene losses between P. tetraurelia and P. sexaurelia representing divergent gene resolutions (i.e., silencing of alternative paralogs), as expected for random duplicate loss between these species. Additionally, though P. biaurelia and P. tetraurelia diverged from each other much later, there are still more than 100 cases of divergent resolution between these two species. Taken together, these results indicate that divergent resolution of duplicate genes between lineages acts to reinforce reproductive isolation between species in the Paramecium aurelia complex.
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Affiliation(s)
- Casey L McGrath
- Department of Biology, Indiana University, Bloomington, Indiana 47408, USA
| | - Jean-Francois Gout
- Department of Biology, Indiana University, Bloomington, Indiana 47408, USA
| | - Parul Johri
- Department of Biology, Indiana University, Bloomington, Indiana 47408, USA
| | - Thomas G Doak
- Department of Biology, Indiana University, Bloomington, Indiana 47408, USA; National Center for Genome Analysis Support at Indiana University, Bloomington, Indiana 47408, USA
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, Indiana 47408, USA;
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138
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Patten SA, Armstrong GAB, Lissouba A, Kabashi E, Parker JA, Drapeau P. Fishing for causes and cures of motor neuron disorders. Dis Model Mech 2014; 7:799-809. [PMID: 24973750 PMCID: PMC4073270 DOI: 10.1242/dmm.015719] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Motor neuron disorders (MNDs) are a clinically heterogeneous group of neurological diseases characterized by progressive degeneration of motor neurons, and share some common pathological pathways. Despite remarkable advances in our understanding of these diseases, no curative treatment for MNDs exists. To better understand the pathogenesis of MNDs and to help develop new treatments, the establishment of animal models that can be studied efficiently and thoroughly is paramount. The zebrafish (Danio rerio) is increasingly becoming a valuable model for studying human diseases and in screening for potential therapeutics. In this Review, we highlight recent progress in using zebrafish to study the pathology of the most common MNDs: spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS) and hereditary spastic paraplegia (HSP). These studies indicate the power of zebrafish as a model to study the consequences of disease-related genes, because zebrafish homologues of human genes have conserved functions with respect to the aetiology of MNDs. Zebrafish also complement other animal models for the study of pathological mechanisms of MNDs and are particularly advantageous for the screening of compounds with therapeutic potential. We present an overview of their potential usefulness in MND drug discovery, which is just beginning and holds much promise for future therapeutic development.
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Affiliation(s)
- Shunmoogum A Patten
- Department of Neuroscience, FRQS Groupe de Recherche sur le Système Nerveux Central and CRCHUM, University of Montréal, Montréal, QC H3A 2B4, Canada
| | - Gary A B Armstrong
- Department of Neuroscience, FRQS Groupe de Recherche sur le Système Nerveux Central and CRCHUM, University of Montréal, Montréal, QC H3A 2B4, Canada
| | - Alexandra Lissouba
- Department of Neuroscience, FRQS Groupe de Recherche sur le Système Nerveux Central and CRCHUM, University of Montréal, Montréal, QC H3A 2B4, Canada
| | - Edor Kabashi
- Institut du Cerveau et de la Moelle Épinière, Centre de Recherche, CHU Pitié-Salpétrière, 75013 Paris, France
| | - J Alex Parker
- Department of Neuroscience, FRQS Groupe de Recherche sur le Système Nerveux Central and CRCHUM, University of Montréal, Montréal, QC H3A 2B4, Canada
| | - Pierre Drapeau
- Department of Neuroscience, FRQS Groupe de Recherche sur le Système Nerveux Central and CRCHUM, University of Montréal, Montréal, QC H3A 2B4, Canada.
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139
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Varela M, Diaz-Rosales P, Pereiro P, Forn-Cuní G, Costa MM, Dios S, Romero A, Figueras A, Novoa B. Interferon-induced genes of the expanded IFIT family show conserved antiviral activities in non-mammalian species. PLoS One 2014; 9:e100015. [PMID: 24950240 PMCID: PMC4065003 DOI: 10.1371/journal.pone.0100015] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 05/21/2014] [Indexed: 12/24/2022] Open
Abstract
Interferon-induced proteins with tetratricopeptide repeats (IFITs) are involved in the protective response to viral infection, although the precise mechanism of IFITs for reducing viral proliferation is currently unknown. The interaction with the translation initiation factor eIF-3 or viral proteins and the sequestering of viral RNA have been proposed as potential antiviral functions for these proteins. In humans, four members of this family have been characterized. Nevertheless, information about these proteins in fish is almost non-existent. Exploiting the conservation of synteny between human and zebrafish genomes, we have identified ten members of the IFIT family located on four different chromosomes. The induction of these genes was examined both in vitro and in vivo after interferon (IFN) administration and rhabdovirus challenge. Whereas an induction of IFIT genes was observed after interferon treatments (IFNΦ1, IFNΦ2 and IFNΦ3), the viral infection did not affect these IFN-induced genes in vitro, and even reduced the IFN-induced expression of these genes. The response was largely different in vivo, with a broad up-regulation of IFIT genes after viral challenge. In addition, three selected IFITs were cloned in an expression vector and microinjected into zebrafish larvae to examine the protective effect of IFITs upon viral infection. Reduction in the mortality rate was observed confirming a conserved antiviral function in non-mammalian species.
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Affiliation(s)
- Mónica Varela
- Instituto de Investigaciones Marinas (IIM), CSIC, Vigo, Spain
| | | | | | | | - Maria M. Costa
- Instituto de Investigaciones Marinas (IIM), CSIC, Vigo, Spain
| | - Sonia Dios
- Instituto de Investigaciones Marinas (IIM), CSIC, Vigo, Spain
| | | | | | - Beatriz Novoa
- Instituto de Investigaciones Marinas (IIM), CSIC, Vigo, Spain
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140
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Immediate and long-term consequences of vascular toxicity during zebrafish development. Reprod Toxicol 2014; 48:51-61. [PMID: 24907688 DOI: 10.1016/j.reprotox.2014.05.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/21/2014] [Accepted: 05/27/2014] [Indexed: 01/02/2023]
Abstract
Proper formation of the vascular system is necessary for embryogenesis, and chemical disruption of vascular development may be a key event driving developmental toxicity. In order to test the effect of environmental chemicals on this critical process, we evaluated a quantitative assay in transgenic zebrafish using angiogenesis inhibitors that target VEGFR2 (PTK787) or EGFR (AG1478). Both PTK787 and AG1478 exposure impaired intersegmental vessel (ISV) sprouting, while AG1478 also produced caudal and pectoral fin defects at concentrations below those necessary to blunt ISV morphogenesis. The functional consequences of vessel toxicity during early development included decreased body length and survival in juvenile cohorts developmentally exposed to inhibitor concentrations sufficient to completely block ISV sprouting angiogenesis. These data show that concentration-dependent disruption of the presumed targets for these inhibitors produce adverse outcomes at advanced life stages.
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141
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Lantz-McPeak S, Guo X, Cuevas E, Dumas M, Newport GD, Ali SF, Paule MG, Kanungo J. Developmental toxicity assay using high content screening of zebrafish embryos. J Appl Toxicol 2014; 35:261-72. [PMID: 24871937 DOI: 10.1002/jat.3029] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 04/18/2014] [Accepted: 04/18/2014] [Indexed: 01/06/2023]
Abstract
Typically, time-consuming standard toxicological assays using the zebrafish (Danio rerio) embryo model evaluate mortality and teratogenicity after exposure during the first 2 days post-fertilization. Here we describe an automated image-based high content screening (HCS) assay to identify the teratogenic/embryotoxic potential of compounds in zebrafish embryos in vivo. Automated image acquisition was performed using a high content microscope system. Further automated analysis of embryo length, as a statistically quantifiable endpoint of toxicity, was performed on images post-acquisition. The biological effects of ethanol, nicotine, ketamine, caffeine, dimethyl sulfoxide and temperature on zebrafish embryos were assessed. This automated developmental toxicity assay, based on a growth-retardation endpoint should be suitable for evaluating the effects of potential teratogens and developmental toxicants in a high throughput manner. This approach can significantly expedite the screening of potential teratogens and developmental toxicants, thereby improving the current risk assessment process by decreasing analysis time and required resources.
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Affiliation(s)
- Susan Lantz-McPeak
- Division of Neurotoxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
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142
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Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence. Genetics 2014; 197:1417-28. [PMID: 24840360 DOI: 10.1534/genetics.114.163287] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Paramecium has long been a model eukaryote. The sequence of the Paramecium tetraurelia genome reveals a history of three successive whole-genome duplications (WGDs), and the sequences of P. biaurelia and P. sexaurelia suggest that these WGDs are shared by all members of the aurelia species complex. Here, we present the genome sequence of P. caudatum, a species closely related to the P. aurelia species group. P. caudatum shares only the most ancient of the three WGDs with the aurelia complex. We found that P. caudatum maintains twice as many paralogs from this early event as the P. aurelia species, suggesting that post-WGD gene retention is influenced by subsequent WGDs and supporting the importance of selection for dosage in gene retention. The availability of P. caudatum as an outgroup allows an expanded analysis of the aurelia intermediate and recent WGD events. Both the Guanine+Cytosine (GC) content and the expression level of preduplication genes are significant predictors of duplicate retention. We find widespread asymmetrical evolution among aurelia paralogs, which is likely caused by gradual pseudogenization rather than by neofunctionalization. Finally, cases of divergent resolution of intermediate WGD duplicates between aurelia species implicate this process acts as an ongoing reinforcement mechanism of reproductive isolation long after a WGD event.
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143
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Silva IAL, Cox CJ, Leite RB, Cancela ML, Conceição N. Evolutionary conservation of TFIIH subunits: implications for the use of zebrafish as a model to study TFIIH function and regulation. Comp Biochem Physiol B Biochem Mol Biol 2014; 172-173:9-20. [PMID: 24731924 DOI: 10.1016/j.cbpb.2014.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 03/24/2014] [Accepted: 03/27/2014] [Indexed: 11/28/2022]
Abstract
Transcriptional factor IIH (TFIIH) is involved in cell cycle regulation, nucleotide excision repair, and gene transcription. Mutations in three of its subunits, XPB, XPD, and TTDA, lead to human recessive genetic disorders such as trichothiodystrophy and xeroderma pigmentosum, the latter of which is sometimes associated with Cockayne's syndrome. In the present study, we investigate the sequence conservation of TFIIH subunits among several teleost fish species and compare their characteristics and putative regulation by transcription factors to those of human and zebrafish. We report the following findings: (i) comparisons among protein sequences revealed a high sequence identity for each TFIIH subunit analysed; (ii) among transcription factors identified as putative regulators, OCT1 and AP1 have the highest binding-site frequencies in the promoters of TFIIH genes, and (iii) TFIIH genes have alternatively spliced isoforms. Finally, we compared the protein primary structure in human and zebrafish of XPD and XPB - two important ATP-dependent helicases that catalyse the unwinding of the DNA duplex at promoters during transcription - highlighting the conservation of domain regions such as the helicase domains. Our study suggests that zebrafish, a widely used model for many human diseases, could also act as an important model to study the function of TFIIH complex in repair and transcription regulation in humans.
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Affiliation(s)
- I A L Silva
- Department of Biomedical Sciences and Medicine, University of Algarve, Faro, Portugal; Centre of Marine Sciences (CCMAR), University of Algarve, Faro, Portugal
| | - C J Cox
- Centre of Marine Sciences (CCMAR), University of Algarve, Faro, Portugal
| | - R B Leite
- Centre of Marine Sciences (CCMAR), University of Algarve, Faro, Portugal
| | - M L Cancela
- Department of Biomedical Sciences and Medicine, University of Algarve, Faro, Portugal; Centre of Marine Sciences (CCMAR), University of Algarve, Faro, Portugal
| | - N Conceição
- Centre of Marine Sciences (CCMAR), University of Algarve, Faro, Portugal.
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144
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Zizioli D, Guarienti M, Tobia C, Gariano G, Borsani G, Bresciani R, Ronca R, Giacopuzzi E, Preti A, Gaudenzi G, Belleri M, Di Salle E, Fabrias G, Casas J, Ribatti D, Monti E, Presta M. Molecular cloning and knockdown of galactocerebrosidase in zebrafish: New insights into the pathogenesis of Krabbe's disease. Biochim Biophys Acta Mol Basis Dis 2014; 1842:665-75. [DOI: 10.1016/j.bbadis.2014.01.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 12/17/2013] [Accepted: 01/15/2014] [Indexed: 11/30/2022]
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145
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Ali S, Aalders J, Richardson MK. Teratological effects of a panel of sixty water-soluble toxicants on zebrafish development. Zebrafish 2014; 11:129-41. [PMID: 24650241 DOI: 10.1089/zeb.2013.0901] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The zebrafish larva is a promising whole-animal model for safety pharmacology, environmental risk assessment, and developmental toxicity. This model has been used for the high-throughput toxicity screening of various compounds. Our aim here is to identify possible phenotypic markers of teratogenicity in zebrafish embryos that could be used for the assaying compounds for reproductive toxicity. We have screened a panel of 60 water-soluble toxicants to examine their effects on zebrafish development. A total of 22,080 wild-type zebrafish larvae were raised in 250 μL defined buffer in 96-well plates at a plating density of one embryo per well. They were exposed for a 96-h period starting at 24 h post-fertilization. A logarithmic concentration series was used for range-finding, followed by a narrower geometric series for developmental toxicity assessment. A total of 9017 survivors were analyzed at 5 days post-fertilization for nine phenotypes, namely, (1) normal, (2) pericardial oedema, (3) yolk sac oedema, (4) melanophores dispersed, (5) bent tail tip, (6) bent body axis, (7) abnormal Meckel's cartilage, (8) abnormal branchial arches, and (9) uninflated swim bladder. For each toxicant, the EC50 (concentration required to produce one or more of these abnormalities in 50% of embryos) was also calculated. For the majority of toxicants (55/60) there was, at the population level, a statistically significant, concentration-dependent increase in the incidence of abnormal phenotypes among survivors. The commonest abnormalities were pericardial oedema, yolk sac oedema, dispersed melanophores, and uninflated swim bladder. It is possible therefore that these could prove to be general indicators of reproductive toxicity in the zebrafish embryo assay.
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Affiliation(s)
- Shaukat Ali
- 1 Sylvius Laboratory, Institute of Biology, Leiden University , Leiden, The Netherlands
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146
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ACF7 is a hair-bundle antecedent, positioned to integrate cuticular plate actin and somatic tubulin. J Neurosci 2014; 34:305-12. [PMID: 24381291 DOI: 10.1523/jneurosci.1880-13.2014] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The precise morphology of the mechanosensitive hair bundle requires seamless integration of actin and microtubule networks. Here, we identify Acf7a (actin crosslinking family protein 7a) as a protein positioned to bridge these distinct cytoskeletal networks in hair cells. By imaging Acf7a-Citrine fusion protein in zebrafish and immunolabeling of vestibular and cochlear mouse hair cells, we show that Acf7a and ACF7 circumscribe, underlie, and are interwoven into the cuticular plate (CP), and they also encircle the basal body of the kinocilium. In cochlear hair cells, ACF7 localization is graded, with the highest concentration near each fonticulus--an area free of F-actin in the region of the CP that contains the basal body. During hair-cell development and regeneration, Acf7a precedes formation of the hair bundle and CP. Finally, electron tomography demonstrates that the ends of microtubules insert into the CP and are decorated with filamentous linkers connecting microtubules to the CP. These observations are consistent with ACF7 being a linker protein, which may shape the cytoskeleton of the hair cell early during hair-bundle genesis.
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147
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Mwafi N, Beretta CA, Paolini A, Carl M. Divergent Wnt8a gene expression in teleosts. PLoS One 2014; 9:e85303. [PMID: 24465531 PMCID: PMC3896364 DOI: 10.1371/journal.pone.0085303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 11/26/2013] [Indexed: 12/02/2022] Open
Abstract
The analysis of genes in evolutionarily distant but morphologically similar species is of major importance to unravel the changes in genomes over millions of years, which led to gene silencing and functional diversification. We report the analysis of Wnt8a gene expression in the medakafish and provide a detailed comparison to other vertebrates. In all teleosts analyzed there are two paralogous Wnt8a copies. These show largely overlapping expression in the early developing zebrafish embryo, an evolutionarily distant relative of medaka. In contrast to zebrafish, we find that both maternal and zygotic expression of particularly one Wnt8a paralog has diverged in medaka. While Wnt8a1 expression is mostly conserved at early embryonic stages, the expression of Wnt8a2 differs markedly. In addition, both genes are distinctly expressed during organogenesis unlike the zebrafish homologs, which may hint at the emergence of functional diversification of Wnt8a ligands during evolution.
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Affiliation(s)
- Nesrin Mwafi
- Heidelberg University, Medical Faculty Mannheim, Department of Cell and Molecular Biology, Mannheim, Germany
| | - Carlo A. Beretta
- Heidelberg University, Medical Faculty Mannheim, Department of Cell and Molecular Biology, Mannheim, Germany
| | - Alessio Paolini
- Heidelberg University, Medical Faculty Mannheim, Department of Cell and Molecular Biology, Mannheim, Germany
| | - Matthias Carl
- Heidelberg University, Medical Faculty Mannheim, Department of Cell and Molecular Biology, Mannheim, Germany
- * E-mail:
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148
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Dufresne F, Stift M, Vergilino R, Mable BK. Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools. Mol Ecol 2013; 23:40-69. [DOI: 10.1111/mec.12581] [Citation(s) in RCA: 248] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 10/29/2013] [Accepted: 10/30/2013] [Indexed: 12/19/2022]
Affiliation(s)
- France Dufresne
- Département de Biologie; Université du Québec à Rimouski; Québec QC Canada G5L 3A1
| | - Marc Stift
- Department of Biology; University of Konstanz; Konstanz D 78457 Germany
| | - Roland Vergilino
- Department of Integrative Biology; University of Guelph; Guelph ON Canada N1G 2W1
| | - Barbara K. Mable
- Institute of Biodiversity; Animal Health and Comparative Medicine; College of Medical, Veterinary and Life Sciences; University of Glasgow; Glasgow UK
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149
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Abstract
In recent years, zebrafish, and to a lesser extent medaka, have become widely used small animal models for human diseases. These organisms have convincingly demonstrated the usefulness of fish for improving our understanding of the molecular and cellular mechanisms leading to pathological conditions, and for the development of new diagnostic and therapeutic tools. Despite the usefulness of zebrafish and medaka in the investigation of a wide spectrum of traits, there is evidence to suggest that other fish species could be better suited for more targeted questions. With the emergence of new, improved sequencing technologies that enable genomic resources to be generated with increasing efficiency and speed, the potential of non-mainstream fish species as disease models can now be explored. A key feature of these fish species is that the pathological condition that they model is often related to specific evolutionary adaptations. By exploring these adaptations, new disease-causing and disease-modifier genes might be identified; thus, diverse fish species could be exploited to better understand the complexity of disease processes. In addition, non-mainstream fish models could allow us to study the impact of environmental factors, as well as genetic variation, on complex disease phenotypes. This Review will discuss the opportunities that such fish models offer for current and future biomedical research.
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Affiliation(s)
- Manfred Schartl
- Department Physiological Chemistry, Biocenter, University of Würzburg, and Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, 97078 Würzburg, Germany
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150
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Mmp17b is essential for proper neural crest cell migration in vivo. PLoS One 2013; 8:e76484. [PMID: 24098510 PMCID: PMC3788140 DOI: 10.1371/journal.pone.0076484] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 08/27/2013] [Indexed: 11/24/2022] Open
Abstract
The extracellular matrix plays a critical role in neural crest (NC) cell migration. In this study, we characterize the contribution of the novel GPI-linked matrix metalloproteinase (MMP) zebrafish mmp17b. Mmp17b is expressed post-gastrulation in the developing NC. Morpholino inactivation of mmp17b function, or chemical inhibition of MMP activity results in aberrant NC cell migration with minimal change in NC proliferation or apoptosis. Intriguingly, a GPI anchored protein with metalloproteinase inhibitor properties, Reversion-inducing-Cysteine-rich protein with Kazal motifs (RECK), which has previously been implicated in NC development, is expressed in close apposition to NC cells expressing mmp17b, raising the possibility that these two gene products interact. Consistent with this possibility, embryos silenced for mmp17b show defective development of the dorsal root ganglia (DRG), a crest-derived structure affected in RECK mutant fish sensory deprived (sdp). Taken together, this study has identified the first pair of MMP, and their putative MMP inhibitor RECK that functions together in NC cell migration.
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