- About this Journal ·
- Abstracting and Indexing ·
- Aims and Scope ·
- Annual Issues ·
- Article Processing Charges ·
- Articles in Press ·
- Author Guidelines ·
- Bibliographic Information ·
- Citations to this Journal ·
- Contact Information ·
- Editorial Board ·
- Editorial Workflow ·
- Free eTOC Alerts ·
- Publication Ethics ·
- Reviewers Acknowledgment ·
- Submit a Manuscript ·
- Subscription Information ·
- Table of Contents
International Journal of Evolutionary Biology
Volume 2012 (2012), Article ID 548081, 8 pages
Investigating the Relationship between Topology and Evolution in a Dynamic Nematode Odor Genetic Network
1Genome Evolution Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
2Department of Biological Sciences, The George Washington University, 333 Lisner Hall, 2023 G Street NW, Washington, DC 20052, USA
3Institute for Neuroscience, The George Washington University, 636 Ross Hall, 2300 I Street NW, Washington, DC 20037, USA
Received 17 May 2012; Revised 6 August 2012; Accepted 29 August 2012
Academic Editor: Amitabh Joshi
Copyright © 2012 David A. Fitzpatrick and Damien M. O'Halloran. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- S. Ward, “Chemotaxis by the nematode Caenorhabditis elegans: identification of attractants and analysis of the response by use of mutants,” Proceedings of the National Academy of Sciences of the United States of America, vol. 70, no. 3, pp. 817–821, 1973.
- D. B. Dusenbery, “Countercurrent separation: a new method for studying behavior of small aquatic organisms,” Proceedings of the National Academy of Sciences of the United States of America, vol. 70, no. 5, pp. 1349–1352, 1973.
- C. I. Bargmann and H. R. Horvitz, “Chemosensory neurons with overlapping functions direct chemotaxis to multiple chemicals in C. elegans,” Neuron, vol. 7, no. 5, pp. 729–742, 1991.
- C. I. Bargmann, E. Hartwieg, and H. R. Horvitz, “Odorant-selective genes and neurons mediate olfaction in C. elegans,” Cell, vol. 74, no. 3, pp. 515–527, 1993.
- A. O. W. Stretton, R. E. Davis, and J. D. Angstadt, “Neural control of behaviour in Ascaris,” Trends in Neurosciences, vol. 8, no. 6, pp. 294–300, 1985.
- L. A. Perkins, E. M. Hedgecock, J. N. Thomson, and J. G. Culotti, “Mutant sensory cilia in the nematode Caenorhabditis elegans,” Developmental Biology, vol. 117, no. 2, pp. 456–487, 1986.
- S. M. Kroetz, J. Srinivasan, J. Yaghoobian, P. W. Sternberg, and R. L. Hong, “The cGMP signaling pathway affects feeding behavior in the necromenic nematode Pristionchus pacificus,” PLoS ONE, vol. 7, no. 4, Article ID e34464, 2012.
- R. L. Hong, H. Witte, and R. J. Sommer, “Natural variation in Pristionchus pacificus insect pheromone attraction involves the protein kinase EGL-4,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 22, pp. 7779–7784, 2008.
- C. Dieterich, S. W. Clifton, L. N. Schuster et al., “The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism,” Nature Genetics, vol. 40, no. 10, pp. 1193–1198, 2008.
- R. J. Sommer, “Pristionchus pacificus,” WormBook, vol. 14, pp. 1–8, 2006.
- S. Kryazhimskiy and J. B. Plotkin, “The population genetics of dN/dS,” PLoS Genetics, vol. 4, no. 12, Article ID e1000304, 2008.
- G. Östlund, T. Schmitt, K. Forslund et al., “Inparanoid 7: new algorithms and tools for eukaryotic orthology analysis,” Nucleic Acids Research, vol. 38, no. 1, pp. D196–D203, 2009.
- L. Li, C. J. Stoeckert Jr., and D. S. Roos, “OrthoMCL: identification of ortholog groups for eukaryotic genomes,” Genome Research, vol. 13, no. 9, pp. 2178–2189, 2003.
- A. Schneider, C. Dessimoz, and G. H. Gonnet, “OMA Browser—exploring orthologous relations across 352 complete genomes,” Bioinformatics, vol. 23, no. 16, pp. 2180–2182, 2007.
- K. Yook, T. W. Harris, T. Bieri et al., “WormBase 2012: more genomes, more data, new website,” Nucleic Acids Research, vol. 40, no. D1, pp. D735–D741, 2012.
- S. F. Altschul, T. L. Madden, A. A. Schäffer et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Research, vol. 25, no. 17, pp. 3389–3402, 1997.
- R. C. Edgar, “MUSCLE: multiple sequence alignment with high accuracy and high throughput,” Nucleic Acids Research, vol. 32, no. 5, pp. 1792–1797, 2004.
- S. Guindon and O. Gascuel, “A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood,” Systematic Biology, vol. 52, no. 5, pp. 696–704, 2003.
- Z. Yang and R. Nielsen, “Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models,” Molecular Biology and Evolution, vol. 17, no. 1, pp. 32–43, 2000.
- Z. Yang, “PAML: a program package for phylogenetic analysis by maximum likelihood,” Computer Applications in the Biosciences, vol. 13, no. 5, pp. 555–556, 1997.
- P. Librado and J. Rozas, “DnaSP v5: a software for comprehensive analysis of DNA polymorphism data,” Bioinformatics, vol. 25, no. 11, pp. 1451–1452, 2009.
- P. Shannon, A. Markiel, O. Ozier et al., “Cytoscape: a software environment for integrated models of biomolecular interaction networks,” Genome Research, vol. 13, no. 11, pp. 2498–2504, 2003.
- E. R. Troemel, B. E. Kimmel, and C. I. Bargmann, “Reprogramming chemotaxis responses: sensory neurons define olfactory preferences in C. elegans,” Cell, vol. 91, no. 2, pp. 161–169, 1997.
- H. A. Colbert and C. I. Bargmann, “Odorant-specific adaptation pathways generate olfactory plasticity in C. elegans,” Neuron, vol. 14, no. 4, pp. 803–812, 1995.
- N. D. L'Etoile, C. M. Coburn, J. Eastham, A. Kistler, G. Gallegos, and C. I. Bargmann, “The cyclic GMP-dependent protein kinase EGL-4 regulates olfactory adaptation in C. elegans,” Neuron, vol. 36, no. 6, pp. 1079–1089, 2002.
- K. Roayaie, J. G. Crump, A. Sagasti, and C. I. Bargmann, “The Gα protein ODR-3 mediates olfactory and nociceptive function and controls cilium morphogenesis in C. elegans olfactory neurons,” Neuron, vol. 20, no. 1, pp. 55–67, 1998.
- D. M. Ferkey, R. Hyde, G. Haspel et al., “C. elegans G protein regulator RGS-3 controls sensitivity to sensory stimuli,” Neuron, vol. 53, no. 1, pp. 39–52, 2007.
- D. A. Birnby, E. M. Link, J. J. Vowels, H. Tian, P. L. Colacurcio, and J. H. Thomas, “A transmembrane guanylyl cyclase (DAF-11) and Hsp90 (DAF-21) regulate a common set of chemosensory behaviors in Caenorhabditis elegans,” Genetics, vol. 155, no. 1, pp. 85–104, 2000.
- M. Matsuki, H. Kunitomo, and Y. Iino, “Goα regulates olfactory adaptation by antagonizing G qα-DAG signaling in Caenorhabditis elegans,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 4, pp. 1112–1117, 2006.
- W. M. Nuttley, S. Harbinder, and D. van der Kooy, “Regulation of distinct attractive and aversive mechanisms mediating benzaldehyde chemotaxis in Caenorhabditis elegans,” Learning and Memory, vol. 8, no. 3, pp. 170–181, 2001.
- N. D. L'Etoile and C. I. Bargmann, “Olfaction and odor discrimination are mediated by the C. elegans guanylyl cyclase ODR-1,” Neuron, vol. 25, no. 3, pp. 575–586, 2000.
- J. Y. Sze and G. Ruvkun, “Activity of the Caenorhabditis elegans UNC-86 POU transcription factor modulates olfactory sensitivity,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 16, pp. 9560–9565, 2003.
- C. M. Coburn and C. I. Bargmann, “A putative cyclic nucleotide-gated channel is required for sensory development and function in C. elegans,” Neuron, vol. 17, no. 4, pp. 695–706, 1996.
- S. A. Daniels, M. Ailion, J. H. Thomas, and P. Sengupta, “egl-4 Acts through a transforming growth factor-β/SMAD pathway in Caenorhabditis elegans to regulate multiple neuronal circuits in response to sensory cues,” Genetics, vol. 156, no. 1, pp. 123–141, 2000.
- G. Jansen, K. L. Thijssen, P. Werner, M. van der Horst, E. Hazendonk, and R. H. A. Plasterk, “The complete family of genes encoding G proteins of Caenorhabditis elegans,” Nature Genetics, vol. 21, no. 4, pp. 414–419, 1999.
- H. Lans, S. Rademakers, and G. Jansen, “A network of stimulatory and inhibitory Gα-subunits regulates olfaction in Caenorhabditis elegans,” Genetics, vol. 167, no. 4, pp. 1677–1687, 2004.
- A. Palmitessa, H. A. Hess, I. A. Bany, Y. M. Kim, M. R. Koelle, and J. L. Benovic, “Caenorhabditus elegans arrestin regulates neural G protein signaling and olfactory adaptation and recovery,” The Journal of Biological Chemistry, vol. 280, no. 26, pp. 24649–24662, 2005.
- A. Kuhara, H. Inada, I. Katsura, and I. Mori, “Negative regulation and gain control of sensory neurons by the C. elegans calcineurin TAX-6,” Neuron, vol. 33, no. 5, pp. 751–763, 2002.
- H. Komatsu, I. Mori, J. S. Rhee, N. Akaike, and Y. Ohshima, “Mutations in a cyclic nucleotide-gated channel lead to abnormal thermosensation and chemosensation in C. elegans,” Neuron, vol. 17, no. 4, pp. 707–718, 1996.
- K. G. Miller, M. D. Emerson, and J. B. Rand, “G(o)α and diacylglycerol kinase negatively regulate the G(q)α pathway in C. elegans,” Neuron, vol. 24, no. 2, pp. 323–333, 1999.
- R. Y. N. Lee, E. R. Sawin, M. Chalfie, H. R. Horvitz, and L. Avery, “EAT-4, a homolog of a mammalian sodium-dependent inorganic phosphate cotransporter, is necessary for glutamatergic neurotransmission in Caenorhabditis elegans,” Journal of Neuroscience, vol. 19, no. 1, pp. 159–167, 1999.
- M. D. Rausher, R. E. Miller, and P. Tiffin, “Patterns of evolutionary rate variation among genes of the anthocyanin biosynthetic pathway,” Molecular Biology and Evolution, vol. 16, no. 2, pp. 266–274, 1999.
- H. Ramsay, L. H. Rieseberg, and K. Ritland, “The correlation of evolutionary rate with pathway position in plant terpenoid biosynthesis,” Molecular Biology and Evolution, vol. 26, no. 5, pp. 1045–1053, 2009.
- D. Waxman and J. R. Peck, “Pleiotropy and the preservation of perfection,” Science, vol. 279, no. 5354, pp. 1210–1213, 1998.
- T. B. Sackton, B. P. Lazzaro, T. A. Schlenke, J. D. Evans, D. Hultmark, and A. G. Clark, “Dynamic evolution of the innate immune system in Drosophila,” Nature Genetics, vol. 39, no. 12, pp. 1461–1468, 2007.
- R. Jovelin, J. P. Dunham, F. S. Sung, and P. C. Phillips, “High nucleotide divergence in developmental regulatory genes contrasts with the structural elements of olfactory pathways in Caenorhabditis,” Genetics, vol. 181, no. 4, pp. 1387–1397, 2009.
- S. Wuchty, “Evolution and topology in the yeast protein interaction network,” Genome Research, vol. 14, no. 7, pp. 1310–1314, 2004.
- H. B. Fraser, A. E. Hirsh, L. M. Steinmetz, C. Scharfe, and M. W. Feldman, “Evolutionary rate in the protein interaction network,” Science, vol. 296, no. 5568, pp. 750–752, 2002.
- D. M. O'Halloran, D. A. Fitzpatrick, G. P. McCormack, J. O. McInerney, and A. M. Burnell, “The molecular phylogeny of a nematode-specific clade of heterotrimeric G-protein α-subunit genes,” Journal of Molecular Evolution, vol. 63, no. 1, pp. 87–94, 2006.
- D. A. Fitzpatrick, D. M. O'Halloran, and A. M. Burnell, “Multiple lineage specific expansions within the guanylyl cyclase gene family,” BMC Evolutionary Biology, vol. 6, article 26, 2006.
- S. Yu, L. Avery, E. Baude, and D. L. Garbers, “Guanylyl cyclase expression in specific sensory neurons: a new family of chemosensory receptors,” Proceedings of the National Academy of Sciences of the United States of America, vol. 94, no. 7, pp. 3384–3387, 1997.