Special Report 19


Ahir BK, Sipes NS, Baker NC, Leung MCK, DeWoskin, R Spencer, Judson RS, Martin MT, Knudsen TB. 2014. Predictive Models of Skeletal Developmental Defects from ToxCast High-Throughput Screening Data. Teratology Society, Bellevue WA, USA.

Ahir B, Rountree MR, DeWoskin RS, Baker NC, Spencer RM, Setzer RW, Lau C, Glazier J, Knudsen TB. Developmental toxicity simulated in a dynamic virtual embryo model of early limb-bud outgrowth. (in preparation).

Allais L, Reynaud L. 2013. Teratology studies in the rabbit. Methods Mol Biol 947:139-156.

Baldock R, Bard J, Kaufman M, Davidson D. A real mouse for your computer. 1992. Bioessays 14:501-502.

Baker NC, Hunter ES, Franzosa JA, Richard A, Judson R, Knudsen T. 2016. ToxCast chemical and bioactivity profiles for in vitro targets in the retinoid signalling system. Poster, SOT 2016, New Orleans, March 2016.

Baker NC, Sipes NS, Grulke CM, Leung MCK, Abbott BD, Judson RS, Knudsen TB. Profiling of cleft palate toxicants in ToxCast. (in preparation).

Bal-Price A, Crofton KM, Leist M, Allen S, Arand M, Buetler T, Delrue N, FitzGerald RE, Hartung T, Heinonen T, Hogberg H, Bennekou SH, Lichtensteiger W, Oggier D, Paparella M, Axelstad M, Piersma A, Rached E, Schilter B, Schmuck G, Stoppini L, Tongiorgi E, Tiramani M, Monnet-Tschudi F, Wilks MF, Ylikomi T, Fritsche E. 2015. International STakeholder NETwork (ISTNET): creating a developmental neurotoxicity (DNT) testing road map for regulatory purposes. Arch Toxicol 89:269-287.

Bard JB. 2005. Anatomics: the intersection of anatomy and bioinformatics. J Anat 206:1-16.

Bard J. 2007. Systems developmental biology: the use of ontologies in annotating models and in identifying gene function within and across species. Mamm Genome 18:402-411.

Bard J. 2012. A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20). J Anat 221:406-416. [EHDAA2: Edinburgh Human Developmental Anatomy Abstract Version 2] Human Developmental Anatomy Ontology (http://purl.bioontology.org/ontology/EHDAA).

Barrow PC (Editor). 2013. Teratogenicity Testing: Methods and Protocols. Methods in Molecular Biology, Volume 947. Humana Press, Springer, New York. , ISBN: 978-1-62703-130-1 (Print) 978-1-62703-131-8 (Online).

Boobis AR, Cohen SM, Dellarco V, McGregor D, Meek ME, Vickers C, Willcocks D, Farland W. 2006. IPCS framework for analyzing the relevance of a cancer mode of action for humans. Crit Rev Toxicol 36:781–792.

Bushnell PJ, Kavlock RJ, Crofton KM, Weiss B, Rice DC. 2010. Behavioral toxicology in the 21st century: challenges and opportunities for behavioral scientists. Summary of a symposium presented at the annual meeting of the Neurobehavioral Teratology Society, June, 2009. Neurotoxicol Teratol 32:313-328.

Chahoud I, Buschmann J, Clark R, Druga A, Falke H, Faqi A, Hansen E, Heinrich-Hirsch B, Hellwig J, Lingk W, Parkinson M, Paumgartten FJ, Pfeil R, Platzek T, Scialli AR, Seed J, Stahlmann R, Ulbrich B, Wu X, Yasuda M, Younes M, Solecki R. 1999. Classification terms in developmental toxicology: need for harmonisation. Report of the Second Workshop on the Terminology in Developmental Toxicology Berlin, 27-28 August 1998. Reprod Toxicol 13:77-82.

Chambers J.E, Greim H, Kendall R.J, Segner H, Sharpe R.M, van der Kraak G. 2014. Human and ecological risk assessment of a crop protection chemical: a case study with the azole fungicide epoxiconazole. Crit Rev Toxicol 44:176-210

Chassaing N, Golzio C, Odent S, Lequeux L, Vigouroux A, Martinovic-Bouriel J, Tiziano FD, Masini L, Piro F, Maragliano G, Delezoide AL, Attié-Bitach T, Manouvrier-Hanu S, Etchevers HC, Calvas P. 2009. Phenotypic spectrum of STRA6 mutations: from Matthew-Wood syndrome to non-lethal anophthalmia. Hum Mutat 30, E673-681.

Correa-Villaseñor A, Cragan J, Kucik J, O'Leary L, Siffel C, Williams L. 2003. The Metropolitan Atlanta Congenital Defects Program: 35 years of birth defects surveillance at the Centers for Disease Control and Prevention. Birth Defects Res A Clin Mol Teratol 67:617-624.

Elmazar MM, Reichert U, Shroot B, Nau H. 1996. Pattern of retinoid-induced teratogenic effects: possible relationship with relative selectivity for nuclear retinoid receptors RAR alpha, RAR beta, and RAR gamma. Teratology 53:158-167.

Emmett SD, West KP Jr. 2014. Gestational vitamin A deficiency: a novel cause of sensorineural hearing loss in the developing world? Med Hypotheses 82:6-10.

Frijters R, Verhoeven S, Alkema W, van Schaik R, Polman J. 2007. Literature-based compound profiling: application to toxicogenomics. Pharmacogenomics 8:1521-1534.

Frijters R, Heupers B, van Beek P, Bouwhuis M, van Schaik R, de Vlieg J, Polman J, Alkema W. 2008. CoPub: a literature-based keyword enrichment tool for microarray data analysis. Nucleic Acids Res 36(Web Server issue):W406-10.

Georgas KM, Armstrong J, Keast JR, Larkins CE, McHugh KM, Southard-Smith EM, Cohn MJ, Batourina E, Dan H, Schneider K, Buehler DP, Wiese CB, Brennan J, Davies JA, Harding SD, Baldock RA, Little MH, Vezina CM, Mendelsohn C. 2015. An illustrated anatomical ontology of the developing mouse lower urogenital tract. Development. 142(10):1893-908.

Hermsen SA, Pronk TE, van den Brandhof EJ, van der Ven LT, Piersma AH. 2012. Triazole-induced gene expression changes in the zebrafish embryo. Reprod Toxicol 34:216-224.

Horton C, Maden M. 1995. Endogenous distribution of retinoids during normal development and teratogenesis in the mouse embryo. Dev Dynam 202:312–323.

Hunter A, Kaufman MH, McKay A, Baldock R, Simmen MW, Bard JBL. 2003. An ontology of human developmental anatomy. J Anat 203(4):347-55.

James CG, Appleton CT, Ulici V, Underhill TM, Beier F. 2005. Microarray analyses of gene expression during chondrocyte differentiation identifies novel regulators of hypertrophy. Mol Biol Cell 16:5316-5333.

Judson R, Houck K, Martin M, Richard AM, Knudsen TB, Shah I, Little S, Wambaugh J, Setzer RW, Kothya P, Phuong J, Filer D, Smith D, Reif D, Rotroff D, Kleinstreuer N, Sipes N, Xia M, Huang R, Crofton K and Thomas RS. 2016. Analysis of the effects of cell stress and cytotoxicity on in vitro assay activity in the ToxCast dataset. Tox Sci 2016 May 20. pii: kfw092. [Epub ahead of print].

Kavlock R, Chandler K, Houck K, Hunter S, Judson R, Kleinstreuer N, Knudsen T, Martin M, Padilla S, Reif D, Richard A, Rotroff D, Sipes N, Dix D. 2012. Update on EPA's ToxCast program: providing high throughput decision support tools for chemical risk management. Chem Res Toxicol 25:1287-1302.

Kleinstreuer NC, Judson RS, Reif DM, Sipes NS, Singh AV, Chandler KJ, Dewoskin R, Dix DJ, Kavlock RJ, Knudsen TB. 2011. Environmental impact on vascular development predicted by high-throughput screening. Environ Health Perspect 119:1596-1603.

Knowlton MN, Li T, Ren Y, Bill BR, Ellis LB, Ekker SC. 2008. A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information. BMC Bioinformatics 9:7.

Knudsen TB, Martin MT, Kavlock RJ, Judson RS, Dix DJ, Singh AV. 2009. Profiling the activity of environmental chemicals in prenatal developmental toxicity studies using the U.S. EPA's ToxRefDB. Reprod Toxicol 28:209-219.

Knudsen TB, Keller DA, Sander M, Carney EW, Doerrer NG, Eaton DL, Fitzpatrick SC, Hastings KL, Mendrick DL, Tice RR, Watkins PB, Whelan M. 2015. FutureTox II: in vitro data and in silico models for predictive toxicology. Toxicol Sci 143:256-67.

Lammer EJ, Chen DT, Hoar RM, Agnish ND, Benke PJ, Braun JT, Curry CJ, Fernhoff PM, Grix AW Jr, Lott IT, Richard JM, Sun SC. 1985. Retinoic acid embryopathy. N Engl J Med 313:837-841.

Leroy M, Allais L. 2013. Teratology studies in the rat. In: Barrow PC (Editor). Teratogenicity Testing: Methods and Protocols. Methods in Molecular Biology, Volume 947, pp.95-109. Humana Press, Springer, New York. , ISBN: 978-1-62703-130-1 (Print) 978-1-62703-131-8 (Online).

Leung MC, Phuong J, Baker NC, Sipes NS, Klinefelter GR, Martin MT, McLaurin KW, Setzer RW, Darney SP, Judson RS, Knudsen TB. 2015. Systems Toxicology of Male Reproductive Development: Profiling 774 Chemicals for Molecular Targets and Adverse Outcomes. Environ Health Perspect 2015 Dec 11. DOI:10.1289/ehp.1510385 (advance publication).

Li H, Rietjens IM, Louisse J, Blok M, Wang X, Snijders L, van Ravenzwaay B. 2015. Use of the ES-D3 cell differentiation assay, combined with the BeWo transport model, to predict relative in vivo developmental toxicity of antifungal compounds. Toxicol In Vitro 29:320-328.

Maden M, Gale E, Kostetskii I, Zile M. 1996. Vitamin A-deficient quail embryos have half a hindbrain and other neural defects. Curr Biol 6:417-426.

Makris SL, Solomon HM, Clark R, Shiota K, Barbellion S, Buschmann J, Ema M, Fujiwara M, Grote K, Hazelden KP, Hew KW, Horimoto M, Ooshima Y, Parkinson M, Wise LD. 2009. Terminology of developmental abnormalities in common laboratory mammals (Version 2). Birth Defects Res B Dev Reprod Toxicol 86:227-327.

Mandal A, Rydeen A, Anderson J, Sorrell MR, Zygmunt T, Torres-Vázquez J, Waxman JS. 2013. Transgenic retinoic acid sensor lines in zebrafish indicate regions of available embryonic retinoic acid. Dev Dynam 242:989-1000.

Marshall H, Morrison A, Studer M, Popperl H, Krumlauf R. 1996. Retinoids and Hox genes. FASEB J 10:969-978.

McCaffery PJ, Adams J, Maden M, Rosa-Molinar E. 2003, Too much of a good thing: retinoic acid as an endogenous regulator of neural differentiation and exogenous teratogen. Eur J Neurosci 18:457-472.

Mineshima H, Fukuta T, Kato E, Uchida K, Aoki T, Matsuno Y, Mori C. 2012. Malformation spectrum induced by ketoconazole after single administration to pregnant rats during the critical period – comparison with vitamin A-induced malformation spectrum. J Appl Toxicol 32:98-107.

Mungall CJ, Torniai C, Gkoutos GV, Lewis SE, Haendel MA. 2012. Uberon, an integrative multi-species anatomy ontology. Genome Biol 13:R5.

Murray-Rust P. 2008. Chemistry for everyone. Nature 451:648-51.

National Library of Medicine MeSH terms. 2015. (http://www.nlm.nih.gov/mesh/2015/mesh_browser/MBrowser.html, accessed 14/01/15)

Niederreither K, Subbarayan V, Dollé P, Chambon P. 1999. Embryonic retinoic acid synthesis is essential for early mouse post-implantation development. Nat Genet 21:444–448.

OECD. 2013a. Guidance Document on Developing and Assessing Adverse Outcome Pathways, ENV/JM/MONO(2013)6. 17-Apr-2013. Organisation for Economic Co-operation and Development, Paris.

OECD. 2013b Users Handbook Supplement to the Guidance Document for Developing and Assessing AOPs [ENV/JM/MONO(2013)6]. Organisation for Economic Co-operation and Development, Paris.

OECD. 2015. Report of the workshop on a Framework for the Development and Use of Integrated Approaches to Testing and Assessment. Series on Testing and Assessment No. 215. ENV/JM/MONO(2015)22. Organisation for Economic Co-operation and Development, Paris.

Pennimpede T, Cameron DA, MacLean GA, Li H, Abu-Abed S, Petkovich M. 2010. The role of CYP26 enzymes in defining appropriate retinoic acid exposure during embryogenesis. Birth Defects Res A Clin Mol Teratol 88:883-894.

Rangarajan J, Luo T, Sargent TD. 2006. PCNS: a novel protocadherin required for cranial neural crest migration and somite morphogenesis in Xenopus. Dev Biol 295:206-218.

Rhinn M, Dollé P. 2012. Retinoic acid signalling during development. Development 139:843-58.

Rijli FM, Gavalas A, Chambon P. 1998. Segmentation and specification in the branchial region of the head: the role of the Hox selector genes. Int J Dev Biol 42:393-401.

Robinson JF, Port JA, Yu X. Faustman EM. 2010. Integrating genetic and toxicogenomic information for determining underlying susceptibility to developmental disorders. Birth Defects Res A Clin Mol Teratol 88:920-930.

Robinson JF, Piersma AH. 2013. Toxicogenomic approaches in developmental toxicology testing. In: Barrow PC (Editor). Teratogenicity Testing: Methods and Protocols. Methods Mol Biol 947:451-473.

Romand R, Sapin V, Dollé P J. 1998. Spatial distributions of retinoic acid receptor gene transcripts in the prenatal mouse inner ear. Comp Neurol. 393:298-308.

Rothman KJ, Moore LL, Singer MR, Nguyen UDT, Mannino S, Milunsky A. 1995. Teratogenicity of high vitamin A intake. N Engl J Med 333:1369-1373.

Rowe A, Richman JM, Brickell PM. 1992. Development of the spatial pattern of retinoic acid receptor-beta transcripts in embryonic chick facial primordia. Development 114:805-813.

Scheuerle A, Tilson H. 2002. Birth defect classification by organ system: a novel approach to heighten teratogenic signalling in a pregnancy registry. Pharmacoepidemiol Drug Saf 11:465-475.

Sipes NS, Martin MT, Reif DM, Kleinstreuer NC, Judson RS, Singh AV, Chandler KJ, Dix DJ, Kavlock RJ, Knudsen TB. 2011. Predictive models of prenatal developmental toxicity from ToxCast high-throughput screening data. Toxicol Sci 124:109-127.

Smith CL, Goldsmith CA, Eppig JT. 2005. The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol 6(1):R7.

Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ; OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S. 2007. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 25:1251-1255.

Solecki R, Bürgin H, Buschmann J, Clark R, Duverger M, Fialkowski O, Guittin P, Hazelden KP, Hellwig J, Hoffmann E, Hofmann T, Hübel U, Khalil S, Lingk W, Mantovani A, Moxon M, Müller S, Parkinson M, Paul M, Paumgartten F, Pfeil R, Platzek T, Rauch-Ernst M, Scheevelenbos A, Seed J, Talsness CE, Yasuda M, Younes M, Chahoud I. 2001. Harmonisation of rat fetal skeletal terminology and classification. Report of the Third Workshop on the Terminology in Developmental Toxicology. Berlin, 14-16 September 2000. Reprod Toxicol 15:713-721.

Solecki R, Bergmann B, Bürgin H, Buschmann J, Clark R, Druga A, Van Duijnhoven EA, Duverger M, Edwards J, Freudenberger H, Guittin P, Hakaite P, Heinrich-Hirsch B, Hellwig J, Hofmann T, Hübel U, Khalil S, Klaus Am, Kudicke S, Lingk W, Meredith T, Moxon M, Müller S, Paul M, Paumgartten F, Röhrdanz E, Pfeil R, Rauch-Ernst M, Seed J, Spezia F, Vickers C, Woelffel B, Chahoud I. 2003. Harmonization of rat fetal external and visceral terminology and classification. Report of the Fourth Workshop on the Terminology in Developmental Toxicology, Berlin, 18-20 April 2002. Reprod Toxicol 17:625-637.

Solecki R, Barbellion S, Bergmann B, Bürgin H, Buschmann J, Clark R, Comotto L, Fuchs A, Faqi AS, Gerspach R, Grote K, Hakansson H, Heinrich V, Heinrich-Hirsch B, Hofmann T, Hübel U, Inazaki TH, Khalil S, Knudsen TB, Kudicke S, Lingk W, Makris S, Müller S, Paumgartten F, Pfeil R, Rama EM, Schneider S, Shiota K, Tamborini E, Tegelenbosch M, Ulbrich B, van Duijnhoven EA, Wise D, Chahoud I. 2013. Harmonization of description and classification of fetal observations: achievements and problems still unresolved: report of the 7th Workshop on the Terminology in Developmental Toxicology Berlin, 4-6 May 2011. Reprod Toxicol 35:48-55.

Solecki R, Rauch M, Gall A, Buschmann J, Clark R, Fuchs A, Kan H, Heinrich V, Kellner R, Knudsen TB, Li W, Makris SL, Ooshima Y, Paumgartten F, Piersma AH, Schönfelder G, Oelgeschläger M, Schaefer C, Shiota K, Ulbrich B, Ding X, Chahoud I. 2015. Continuing harmonization of terminology and innovations for methodologies in developmental toxicology: Report of the 8th Berlin Workshop on Developmental Toxicity, 14-16 May 2014. Reprod Toxicol 57:140-146.

Tiboni GM, Marotta F, Del Corso A, Giampietro F. 2006. Defining critical periods for itraconazole-induced cleft palate, limb defects and axial skeletal malformations in the mouse. Toxicol Lett 167:8-18.

Tice RR, Austin CP, Kavlock RJ, Bucher JR. 2013. Improving the human hazard characterization of chemicals: a Tox21 update. Environ Health Perspect 121:756-765.

Tonk EC, Pennings JL, Piersma AH. 2015. An adverse outcome pathway framework for neural tube and axial defects mediated by modulation of retinoic acid homeostasis. Reprod Toxicol 55:104-113.

van Dartel DA, Pennings JL, Robinson JF, Kleinjans JC, Piersma AH. 2011. Discriminating classes of developmental toxicants using gene expression profiling in the embryonic stem cell test. Toxicol Lett 201:143-151.

Viallet JP, Dhouailly D. 1994. Retinoic acid and mouse skin morphogenesis. I. Expression pattern of retinoic acid receptor genes during hair vibrissa follicle, plantar, and nasal gland development. J Invest Dermatol 103:116-121.

Villeneuve DL, Crump D, Garcia-Reyero N, Hecker M, Hutchinson TH, LaLone CA, Landesmann B, Lettieri T, Munn S, Nepeska M, Ottinger MA, Vergauwen L, Whelan M. 2014a. Adverse Outcome Pathway Development I: Strategies and Principles. Toxicol Sci 142:312-320.

Villeneuve DL, Crump D, Garcia-Reyero N, Hecker M, Hutchinson TH, LaLone CA, Landesmann B, Lettieri T, Munn S, Nepeska M, Ottinger MA, Vergauwen L, Whelan M. 2014b. Adverse Outcome Pathway Development II: Best Practices. Toxicol Sci 142:321-330.

Werler MM, Lammer EJ, Rosenberg L, Mitchell AA. 1990. Maternal vitamin A supplementation in relation to selected birth defects. Teratology 42:497-503.

White JC, Highland M, Kaiser M, Clagett-Dame M. 2000. Vitamin A deficiency results in the dose-dependent acquisition of anterior character and shortening of the caudal hindbrain of the rat embryo. Dev Biol 220:263–284.

WHO. 2007. Harmonization Project Document No. 4. PART 1: IPCS Framework for Analysing the Relevance of a Cancer Mode of Action for Humans and Case-Studies PART 2: IPCS Framework for Analysing the Relevance of a Non-Cancer Mode of Action for Humans. World Health Organization, Geneva, Switzerland.

WHO. 2009. Global prevalence of vitamin A deficiency in populations at risk 1995–2005. World Health Organization, Geneva, Switzerland.

WHO. 2013. Deafness and hearing loss. World Health Organization, Geneva, Switzerland.

Wise LD, Beck SL, Beltrame D, Beyer BK, Chahoud I, Clark RL, Clark R, Druga AM, Feuston MH, Guittin P, Henwood SM, Kimmel CA, Lindstrom P, Palmer AK, Petrere JA, Solomon HM, Yasuda M, York RG. 1997. Terminology of developmental abnormalities in common laboratory mammals (version 1). Teratology 55:249-292.

Wu S, Fisher J, Naciff J, Laufersweiler M, Lester C, Daston G, Blackburn K. 2013. Framework for identifying chemicals with structural features associated with the potential to act as developmental or reproductive toxicants. Chem Res Toxicol 26:1840-1861.

Zhang Q, Bhattacharya S, Conolly RB, Clewell HJ, Kaminski NE, Andersen ME. 2014. Molecular Signalling Network Motifs Provide a Mechanistic Basis for Cellular Threshold Responses. Environ Health Perspect 122:1261-1270.