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2013
L. Chen, Yang, D. Y., Liu, T. F., Nong, X., Huang, X., Xie, Y., Fu, Y., Zheng, W. P., Zhang, R. H., Wu, X. H., Gu, X. B., Wang, S. X., Peng, X. R., and Yang, G. Y., Synonymous codon usage patterns in different parasitic platyhelminth mitochondrial genomes, vol. 12, pp. 587-596, 2013.
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Genomics 74: 197-210. http://dx.doi.org/10.1006/geno.2001.6531 PMid:11386756   Fadiel AA, Lithwick S and Gamra MM (2002). Codon usage analysis of Ascaris species influence of base and intercodon frequencies on the synonymous codon usage. J. Egypt. Soc. Parasitol. 32: 625-638. PMid:12214939   Fickett JW (1982). Recognition of protein coding regions in DNA sequences. Nucleic Acids Res. 10: 5303-5318. http://dx.doi.org/10.1093/nar/10.17.5303 PMid:7145702 PMCid:320873   Grantham R, Gautier C, Gouy M, Mercier R, et al. (1980). Codon catalog usage and the genome hypothesis. Nucleic Acids Res. 8: r49-r62. http://dx.doi.org/10.1093/nar/8.1.197-c PMid:6986610 PMCid:327256   Hua J and Lee RW (2012). Factors affecting codon bias in the mitochondrial genomes of the streptophyte Mesostigma viride and the chlorophyte Chlamydomonas reinhardtii. J. Eukaryot. Microbiol. 59: 287-289. http://dx.doi.org/10.1111/j.1550-7408.2011.00613.x PMid:22340021   Ikemura T (1981). Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J. Mol. Biol. 151: 389-409. http://dx.doi.org/10.1016/0022-2836(81)90003-6   Jia W and Higgs PG (2008). Codon usage in mitochondrial genomes: distinguishing context-dependent mutation from translational selection. Mol. Biol. Evol. 25: 339-351. http://dx.doi.org/10.1093/molbev/msm259 PMid:18048402   Karlin S and Mrazek J (1996). What drives codon choices in human genes? J. Mol. Biol. 262: 459-472. http://dx.doi.org/10.1006/jmbi.1996.0528 PMid:8893856   Liu H, He R, Zhang H, Huang Y, et al. (2010). Analysis of synonymous codon usage in Zea mays. Mol. Biol. Rep. 37: 677-684. http://dx.doi.org/10.1007/s11033-009-9521-7 PMid:19330534   Liu Q, Feng Y and Xue Q (2004). Analysis of factors shaping codon usage in the mitochondrion genome of Oryza sativa. 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Nature 357: 153-155. http://dx.doi.org/10.1038/357153a0 PMid:1579163   Moriyama EN and Powell JR (1998). Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli. Nucleic Acids Res. 26: 3188-3193. http://dx.doi.org/10.1093/nar/26.13.3188 PMid:9628917 PMCid:147681   Musto H, Cruveiller S, D'Onofrio G, Romero H, et al. (2001). Translational selection on codon usage in Xenopus laevis. Mol. Biol. Evol. 18: 1703-1707. http://dx.doi.org/10.1093/oxfordjournals.molbev.a003958 PMid:11504850   Oresic M and Shalloway D (1998). Specific correlations between relative synonymous codon usage and protein secondary structure. J. Mol. Biol. 281: 31-48. http://dx.doi.org/10.1006/jmbi.1998.1921 PMid:9680473   Osawa S, Ohama T, Yamao F, Muto A, et al. (1988). Directional mutation pressure and transfer RNA in choice of the third nucleotide of synonymous two-codon sets. Proc. Natl. Acad. Sci. U. S. 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Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons. Nucleic Acids Res. 14: 7737-7749. http://dx.doi.org/10.1093/nar/14.19.7737 PMid:3534792 PMCid:311793   Sloan DB and Taylor DR (2010). Testing for selection on synonymous sites in plant mitochondrial DNA: the role of codon bias and RNA editing. J. Mol. Evol. 70: 479-491. http://dx.doi.org/10.1007/s00239-010-9346-y PMid:20424833   Wang B, Liu J, Jin L, Feng XY, et al. (2010). Complex mutation and weak selection together determined the codon usage bias in bryophyte mitochondrial genomes. J. Integr. Plant Biol. 52: 1100-1108. http://dx.doi.org/10.1111/j.1744-7909.2010.00998.x PMid:21106008   Wang B, Yuan J, Liu J, Jin L, et al. (2011). Codon usage bias and determining forces in green plant mitochondrial genomes. J. Integr. Plant Biol. 53: 324-334. http://dx.doi.org/10.1111/j.1744-7909.2011.01033.x PMid:21332641   Whittle CA, Sun Y and Johannesson H (2011). Evolution of synonymous codon usage in Neurospora tetrasperma and Neurospora discreta. Genome Biol. Evol. 3: 332-343. http://dx.doi.org/10.1093/gbe/evr018 PMid:21402862 PMCid:3089379   Wright F (1990). The 'effective number of codons' used in a gene. Gene 87: 23-29. http://dx.doi.org/10.1016/0378-1119(90)90491-9   Xie T and Ding D (1998). The relationship between synonymous codon usage and protein structure. FEBS Lett. 434: 93-96. http://dx.doi.org/10.1016/S0014-5793(98)00955-7   Zhang Y, Liu Y, Liu W, Zhou J, et al. (2011). Analysis of synonymous codon usage in hepatitis A virus. Virol. J. 8: 174. http://dx.doi.org/10.1186/1743-422X-8-174 PMid:21496278 PMCid:3087699   Zhou M and Li X (2009). Analysis of synonymous codon usage patterns in different plant mitochondrial genomes. Mol. Biol. Rep. 36: 2039-2046. http://dx.doi.org/10.1007/s11033-008-9414-1 PMid:19005776
2012
X. J. Chen, Li, Z. B., Chen, L., Cao, Y. Y., and Li, Q. H., Isolation and characterization of new microsatellite markers in the pen shell Atrina pectinata (Pinnidae), vol. 11, pp. 2884-2887, 2012.
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Z. L. Yao, Wang, H., Chen, L., Zhou, K., Ying, C. Q., and Lai, Q. F., Transcriptomic profiles of Japanese medaka (Oryzias latipes) in response to alkalinity stress, vol. 11, pp. 2200-2246, 2012.
Brindley DN and Pilquil C (2009). Lipid phosphate phosphatases and signaling. J. Lipid. Res. 50: S225-S230. http://dx.doi.org/10.1194/jlr.R800055-JLR200 PMid:19066402 PMCid:2674702   Claiborne JB, Edwards SL and Morrison-Shetlar AI (2002). Acid-base regulation in fishes: cellular and molecular mechanisms. J. Exp. Zool. 293: 302-319. http://dx.doi.org/10.1002/jez.10125 PMid:12115903   Dennis G Jr, Sherman BT, Hosack DA, Yang J, et al. (2003). DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 4: 3. http://dx.doi.org/10.1186/gb-2003-4-5-p3   Evans TG (2010). Co-ordination of osmotic stress responses through osmosensing and signal transduction events in fishes. J. Fish Biol. 76: 1903-1925. http://dx.doi.org/10.1111/j.1095-8649.2010.02590.x PMid:20557646   Fiol DF and Kültz D (2007). Osmotic stress sensing and signaling in fishes. FEBS J. 274: 5790-5798. http://dx.doi.org/10.1111/j.1742-4658.2007.06099.x PMid:17944942   Gibson G (2008). The environmental contribution to gene expression profiles. Nat. Rev. Genet. 9: 575-581. http://dx.doi.org/10.1038/nrg2383 PMid:18574472   Gilmour KM and Perry SF (2009). Carbonic anhydrase and acid-base regulation in fish. J. Exp. Biol. 212: 1647-1661. http://dx.doi.org/10.1242/jeb.029181 PMid:19448075   Goss GG, Wood CM, Laurent P and Perry SF (1994). Morphological responses of the rainbow trout (Oncorhynchus mykiss) gill to hyperoxia, base (NaHCO3) and acid (HCl) infusions. Fish Physiol. Biochem. 12: 465-477. http://dx.doi.org/10.1007/BF00004449   Green TJ and Barnes AC (2010). Reduced salinity, but not estuarine acidification, is a cause of immune-suppression in the Sydney rock oyster Saccostrea glomerata. Mar. Ecol. Prog. Ser. 402: 161-170. http://dx.doi.org/10.3354/meps08430   Hirayama M, Nakaniwa M, Mitani H and Watabe S (2005). Gene expression profiles for medaka Olyzias latipes associated with cold and warm temperatures in cDNA microarray. Comp. Biochem. Phys. 141: S354-S355.   Hwang PP and Lee TH (2007). New insights into fish ion regulation and mitochondrion-rich cells. Comp. Biochem. Physiol. A Mol. Integr. Physiol. 148: 479-497. http://dx.doi.org/10.1016/j.cbpa.2007.06.416 PMid:17689996   Inoue K and Takei Y (2002). Diverse adaptability in oryzias species to high environmental salinity. Zoolog. Sci. 19: 727- 734. http://dx.doi.org/10.2108/zsj.19.727 PMid:12149572   Kanehisa M and Goto S (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28: 27-30. http://dx.doi.org/10.1093/nar/28.1.27 PMid:10592173 PMCid:102409   Kang CK, Tsai SC, Lee TH and Hwang PP (2008). Differential expression of branchial Na+/K+-ATPase of two medaka species, Oryzias latipes and Oryzias dancena, with different salinity tolerances acclimated to fresh water, brackish water and seawater. Comp. Biochem. Physiol. A Mol. Integr. Physiol. 151: 566-575. http://dx.doi.org/10.1016/j.cbpa.2008.07.020 PMid:18692588   Kasahara M, Naruse K, Sasaki S, Nakatani Y, et al. (2007). The medaka draft genome and insights into vertebrate genome evolution. Nature 447: 714-719. http://dx.doi.org/10.1038/nature05846 PMid:17554307   Kültz D (2001). Evolution of osmosensory MAP kinase signaling pathways. Am. Zool. 41: 743-757. http://dx.doi.org/10.1668/0003-1569(2001)041[0743:EOOMKS]2.0.CO;2   Kültz D (2005). Molecular and evolutionary basis of the cellular stress response. Annu. Rev. Physiol. 67: 225-257. http://dx.doi.org/10.1146/annurev.physiol.67.040403.103635 PMid:15709958   Kurosawa Y and Hashimoto K (1997). How did the primordial T cell receptor and MHC molecules function initially? Immunol. Cell Biol. 75: 193-196. http://dx.doi.org/10.1038/icb.1997.28 PMid:9107575   Lang F, Bohmer C, Palmada M, Seebohm G, et al. (2006). (Patho)physiological significance of the serum- and glucocorticoid-inducible kinase isoforms. Physiol. Rev. 86: 1151-1178. http://dx.doi.org/10.1152/physrev.00050.2005 PMid:17015487   Lockwood BL, Sanders JG and Somero GN (2010). Transcriptomic responses to heat stress in invasive and native blue mussels (genus Mytilus): molecular correlates of invasive success. J. Exp. Biol. 213: 3548-3558. http://dx.doi.org/10.1242/jeb.046094 PMid:20889835   Loffing J, Flores SY and Staub O (2006). Sgk kinases and their role in epithelial transport. Annu. Rev. Physiol. 68: 461- 490. http://dx.doi.org/10.1146/annurev.physiol.68.040104.131654 PMid:16460280   Parra JEG and Baldisserotto B (2007). Effect of Water pH and Hardness on Survival and Growth of Freshwater Teleosts. In: Fish Osmoregulation (Baldisserotto B, Mancera JM and Kapoor BG, eds.). Science Publishers, Enfield, 139.   Perry SF and Gilmour KM (2006). Acid-base balance and CO2 excretion in fish: unanswered questions and emerging models. Respir. Physiol. Neurobiol. 154: 199-215. http://dx.doi.org/10.1016/j.resp.2006.04.010 PMid:16777496   Podrabsky JE and Somero GN (2004). Changes in gene expression associated with acclimation to constant temperatures and fluctuating daily temperatures in an annual killifish Austrofundulus limnaeus. J. Exp. Biol. 207: 2237-2254. http://dx.doi.org/10.1242/jeb.01016 PMid:15159429   Prophete C, Carlson EA, Li Y, Duffy J, et al. (2006). Effects of elevated temperature and nickel pollution on the immune status of Japanese medaka. Fish Shellfish Immunol. 21: 325-334. http://dx.doi.org/10.1016/j.fsi.2005.12.009 PMid:16529948   Randall DJ and Tsui TK (2006). Tribute to R. G. Boutilier: acid-base transfer across fish gills. J. Exp. Biol. 209: 1179- 1184. http://dx.doi.org/10.1242/jeb.02100 PMid:16547290   Rodrigues PN, Hermsen TT, van Maanen A, Taverne-Thiele AJ, et al. (1998). Expression of MhcCyca class I and class II molecules in the early life history of the common carp (Cyprinus carpio L.). Dev. Comp. Immunol. 22: 493-506. http://dx.doi.org/10.1016/S0145-305X(97)00059-1   Rozen S and Skaletsky HJ (2000). Primer 3 on the WWW for General Users and for Biologist Programmers. In: Bioinformatics Methods and Protocols: Methods in Molecular Biology (Krawetz S and Misener S, eds.). Humana Press, Totowa, 365-386. PMid:10547847   Schmittgen TD and Livak KJ (2008). Analyzing real-time PCR data by the comparative CT method. Nat. Protoc. 3: 1101- 1108. http://dx.doi.org/10.1038/nprot.2008.73 PMid:18546601   Scott GR, Richards JG, Forbush B, Isenring P, et al. (2004). Changes in gene expression in gills of the euryhaline killifish Fundulus heteroclitus after abrupt salinity transfer. Am. J. Physiol. Cell Physiol. 287: C300-C309. http://dx.doi.org/10.1152/ajpcell.00054.2004 PMid:15044150   Takeda H and Shimada A (2010). The art of medaka genetics and genomics: what makes them so unique? Annu. Rev. 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Unusual physiology of scale-less carp, Gymnocypris przewalskii, in Lake Qinghai: a high altitude alkaline saline lake. Comp. Biochem. Physiol. A Mol. Integr. Physiol. 134: 409-421. http://dx.doi.org/10.1016/S1095-6433(02)00317-3   Wilkie MP and Wood CM (1996). The adaptations of fish to extremely alkaline environments. Comp. Biochem. Phys. B 113: 665-673. http://dx.doi.org/10.1016/0305-0491(95)02092-6   Yao ZL, Lai QF, Zhou K, Rizalita RE, et al. (2010). Developmental biology of medaka fish (Oryzias latipes) exposed to alkalinity stress. J. Appl. Ichthyol. 26: 397-402. http://dx.doi.org/10.1111/j.1439-0426.2009.01360.x   Yum S, Woo S, Kagami Y, Park HS, et al. (2010). Changes in gene expression profile of medaka with acute toxicity of Arochlor 1260, a polychlorinated biphenyl mixture. Comp. Biochem. Physiol. C Toxicol. Pharmacol. 151: 51-56.   Zhang Z, Ju Z, Wells MC and Walter RB (2009). Genomic approaches in the identification of hypoxia biomarkers in model fish species. J. Exp. 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2010
X. Z. Kan, Li, X. F., Zhang, L. Q., Chen, L., Qian, C. J., Zhang, X. W., and Wang, L., Characterization of the complete mitochondrial genome of the Rock pigeon, Columba livia (Columbiformes: Columbidae), vol. 9, pp. 1234-1249, 2010.
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